Promethease Report

Version: Promethease 0.1.14

Generated: 2008-05-22 14:36

Infile: C:\Users\andrew\Desktop\genome_Andrew_Yates_20080522130903.txt

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1490 genotypes annotated

Genoset
gs101 This genoset predicts lactose tolerance

Rarest
0.0	rs2072797 (C;C)

			rs2072797, a SNP in the UNC84B gene also known as G671S, is associated with risk for developing Non-Hodgkin Lymphoma based on a study of 458 patients. The odds ratio is 1.50 (CI: 1.12-2.00, p<0.01).
0.0	rs3792876 (C;C)

			rs7528684 rs3792876 and rs2268277 failed to showed a statistically significant association with rheumatoid arthritis rs3792876, a SNP in the SLC22A4 gene, has been associated along with rs2073838 (another SNP in the SLC22A4 gene) with an autoimmune disease, in this case, Crohn's disease, odds ratio = 2.1 (CI = 1.313.39), from 203 cases and 200 controls. The risk allele for rs3792876 appears to be (T).
0.0	rs2476601 (A;A)	>2x risk for T1D, RA, Addison's

			This SNP, located in the PTPN22 gene and also known as R620W, or 1858C>T, may influence Rheumatoid Arthritis and other autoimmune diseases, including but not limited to, multiple sclerosis, Crohn's disease, celiac disease and type-1 diabetes. The risk allele (in dbSNP orientation) is rs2476601(A). Note that rs6679667 and rs2476601 are reported to be perfectly correlated, so SNP determination of one predicts the other. In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for type-1 diabetes for this SNP was recalculated to be 1.98 (CI 1.822.15). rs2476601 was confirmed in another 2007 study to be a risk factor for RA . * confirms the association of rs2476601 rheumatoid arthritis * two copies of the PTPN22 R620W allele more than doubles the ris...
0.0	rs17276358 (G;G)

			[haplogroup:?]
0.0	rs16980391 (A;A)

			[haplogroup:?]
0.0	rs16980586 (G;G)

			[haplogroup:?]
0.0	rs17316007 (A;A)

			[haplogroup:?]
0.0	rs2032596 (C;C)

			[haplogroup:?]
0.0	rs16981311 (C;C)

			[haplogroup:?]
0.0	rs2032598 (T;T)

			[haplogroup:?]
0.0	rs2032673 (T;T)

			[haplogroup:?]
0.0	rs17842518 (G;G)

			[haplogroup:?]
0.0	rs4141886 (A;A)
			[haplogroup:CF]
			[haplogroup:?]
0.0	rs16980588 (G;G)

			[haplogroup:?]
0.0	rs2032609 (C;C)

			[haplogroup:?]
0.0	rs17842387 (A;A)

			[haplogroup:?]
0.0	rs16980598 (G;G)

			[haplogroup:?]
0.0	rs2032607 (C;C)

			[haplogroup:?]
0.0	rs2032680 (A;A)

			[haplogroup:?]
0.0	rs16980396 (T;T)
			[haplogroup:F-R]
			[haplogroup:?]
0.0	rs2032610 (T;T)

			[haplogroup:?]
0.0	rs9786431 (G;G)

			[haplogroup:?]
0.0	rs2032595 (T;T)
			[haplogroup:CR]
			[haplogroup:?]
1.7	rs4877365 (A;A)

			rs4877365 has been linked to Alzheimer's disease
3.3	rs662799 (A;G)

			this snp prevents [http://www.medicalnewstoday.com/medicalnews.php?newsid=67543 weight gain from high fat diets]. rs662799 -1131T>C in APOA5 is present in approximately 13% of this population, modulates the effect of fat intake on BMI and obesity risk in both men and women.
3.3	rs7892900 (C;C)

			[haplogroup:?]
3.3	rs16879498 (C;T)

			[omim:RH-NULL HEMOLYTIC ANEMIA, REGULATOR TYPE]
3.3	rs17316910 (G;G)

			[haplogroup:?]
3.3	rs17703883 (C;C)

			The research paper suggests that the 3 snps rs17703883, rs12594287 and rs16964201 affect bone mineral density in men.
3.4	rs4660646 (G;G)

			Suspected of reproducibility problems based on [http://www.kk.org/quantifiedself/2008/05/testing-genetic-test-chips.php end user analysis] rs11149566 rs4458717 rs4660646 rs754499
3.6	rs2534636 (T;T)

			[haplogroup:?]
5.0	rs806368 (C;C)

			risk of the development of substance dependence significantly increased with the number of 'G' alleles at rs6454674 and SNP8;T/T genotypes had significant interaction effects (p = .0003 for comorbid DD and AD, .0002 for DD, and .007 for AD). SNP3 and SNP8 together exerted stronger genetic effects on SD than either did individually. The peak delta values among all the markers were seen for SNP3 and SNP8 (rs806368)
5.0	rs3816873 (C;C)

			Also known as I128T MTP rare allele of the MTP I128T polymorphism may be protective against impaired glucose tolerance, type-2 diabetes
6.7	rs9264942 (C;C)	90% reduction in HIV viral load
			The rs9264942(C;C) genotype is reported to be associated with a 90% reduction in viral load in HIV-infected individuals. See also rs9264942 and HIV.
			This SNP (C/T) is in 5' region of the HLA-C gene, 35 kb away from transcription initiation in or around the HLA-C gene. 'People with this tiny sequence variation, dubbed rs9264942, appear to have up to 90% less virus in their systems than those who carry other polymorphisms. About 10% of Europeans appear to carry two copies of rs9264942, which leads to an average 90% viral load reduction. About 50% of Europeans carry one copy, which gives a 60% reduction. By comparison, less than 40% of people of African descent appear to carry a single copy of the polymorphism.' [http://www.newscientist.com/article/dn12297-genetic-variation-may-lower-hiv-load-by-90.html Genetic variation may lower HIV load by 90%] They are referring to the (C;C) genotype giving a 90% reduction and the (C;T) giving a 60% r...
6.7	rs1799724 (C;T)	if ApoE4(-), 1.6x risk of AD; if (+), 6.6x risk

			rs1799724, a SNP in the tumor necrosis factor TNF gene, was found in a study of ~500 Caucasians to be both an independent risk factor for the development of Alzheimer's disease and also a modifier of the risk for individuals carrying ApoE4 alleles. On it's own, the rs1799724(T) allele led to an odds ratio of 1.63 (CI: 1.13-2.34, p=0.009). In carriers of ApoE4 alleles, the odds ratio changed from 2.92 (CI: 2.00-4.27) in the absence of rs1799724(T) to an OR of 6.65 (CI: 3.26-13.55, p=0.03) in its presence.
6.7	rs4794067 (C;C)	2.1x risk for AIA

			rs4794067(C;C) and rs4794067(C;T) genotypes for the TBX21 gene are calculated to be at 2.15 fold higher risk (CI: 1.26-3.64) for aspirin-induced asthma (AIA) compared to rs4794067(T;T) homozygotes, based on a study of 72 patients vs 640 controls in a study of a Japanese population. Note that in this population, but perhaps not others, linkage disequilibrium exists between this SNP located upstream of the gene, rs4794067, and a common synonymous SNP located in the first exon, rs2074190, with a predictive accuracy of 92%.
8.3	rs7756992 (G;G)

			rs7756992 significantly p = 0.0363 associated with type-2 diabetes in 1,630 Japanese subjects and in 1,064 controls 1,638 type 2 diabetes patients and 1,858 controls rs7756992 non-significant T2D and normal glucose tolerant (NGT) individuals. (3,295 T2D and 3,595 NGT), strong associations with T2D were found for CDKAL1 (OR(rs7756992) = 1.30[1.19-1.42], P = 2.3x10(-9)) CDKN2A/2B (OR(rs10811661) = 0.74[0.66-0.82], P = 3.5x10(-8)) IGFBP2 (OR(rs1470579) = 1.17[1.07-1.27], P = 0.0003) SNPs. T2D risk increased strongly when risk alleles, including the previously discovered T2D-associated TCF7L2 rs7903146 SNP, were combined (8.68-fold for the 14% of French individuals carrying 18 to 30 risk alleles with an allelic OR of 1.24)
8.3	rs6897690 (A;A)

			schizophrenia rs7715300 (p = 0.001) and rs6897690 (p = 0.032)
8.3	rs11868035 (A;A)	1.19x increased risk for T2D

			rs11868035 is one of several SNPs associated with the SREBF1 gene that show a modest association with type-2 diabetes. A study of ~2,000 Caucasian patients (and 10,000+ controls) led to an odds ratio of 1.19 (CI: 1.07-1.33, p=0.002) for the minor (risk) allele, rs11868035(A), in the orientation as in dbSNP.
8.3	rs569108 (C;T)	3x risk

			rs569108, a SNP in the MS4A2 gene, has been linked in a Japanese population to a predisposition to childhood asthma, with an odds ratio of 3 [PMID 8842731, PMID 8968765]. The risk allele in dbSNP orientation is (C). [Note: no (C;C) homozygotes were observed in this population.]
8.3	rs4712523 (G;G)

			associated with type-2 diabetes
10.0	rs9295536 (A;A)	2x increased risk for neuroblastoma

			SNPs clustered in one region of chromosome 6p22 have been linked to increased risk for the exceedingly rare childhood cancer known as neuroblastoma. A study involving 720 patients determined that rs9295536(A;A) genotypes had increased likelihood of neuroblastoma development (odds ratio 1.93, CI: 1.55 to 2.40, p=8 x 10^-8). At-risk homozygotes diagnosed with neuroblastoma had, on average, more malignant clinical presentation, more aggressive disease, and poorer long-term survival. For more information on this cluster of SNPs, see rs6939340.
10.0	rs1799836 (G;G)

			Parkinson's disease The risk alleles for each SNP identified from conditional logistic regression, rs1721100 C, rs1721082 T and rs1799836 A, are consistent with previous reports. Significant interaction between this MAOB SNP and a FGF20 SNP, rs1721100 was also noticed.
10.5	rs6596189 (C;T)

			Individuals homozygous or heterozygous for the rs11959298(A)-rs6596189(C) haplotype risk allele were 2.54 and 1.59 fold more likely to have autism, respectively, compared to rs11959298(G)-rs6596189(T) carriers. Note/caveat emptor: ~90% of the world's population carries what the authors from this for-profit genetic testing company call the 'risk haplotype', yet the frequency of autism is less than 1% (perhaps 1 in 150).
11.7	rs2987983 (A;A)	(?)normal risk

			In one large Swedish study, men with one or two rs2987983(C) alleles were reported to be at somewhat increased (odds ratio 1.22) risk for Prostate cancer compared to men homozygous for the wild type rs2987983(T) allele, however the risk can be reduced by adding phytoestrogens to the diet.
11.7	rs8192284 (C;C)

			linked to diabetes by
11.7	rs3751812 (T;T)

			Within the FTO gene, many SNPs appear to be co-inherited. The SNP showing the strongest association with body weight (i.e. body mass index, BMI) is not rs3751812, although this SNP is one of the co-inherited SNPs in the FTO gene region. For more information, refer to the FTO gene or the most studied FTO SNPs, rs9930506 or rs9939609. implicated for african americans
11.7	rs8050136 (A;A)

			This SNP is in a linkage block in the FTO gene with rs1121980; see rs1121980 for the association of this block with early onset obesity since it showed the strongest association. This SNP did not show any association with obesity, type-2 diabetes or any other related traits in a study of 3,210 Chinese subjects. Furthermore, the minor allele frequency was much lower in Chinese populations compared to populations of European descent.
11.7	rs3922812 (T;T)

			Associated with type-2 diabetes in a Mexican-American population.
11.9	rs2229765 (A;A)

			rs2229765(A;A) associated with ischemic stroke (OR = 1.641, P = 0.022) in a Chinese population
13.3	rs2298668 (A;C)

			Women with the snp has been linked to significant risk of a premature birth These [http://www.eurekalert.org/pub_releases/2006-08/vcu-gvi081606.php press] [http://www.eurekalert.org/pub_releases/2006-08/modb-rdg081706.php releases] explain it more simply The risky variation is 3x more common in women of african descent. *rs2298668 Prolylcarboxypepdiase E112D (rs2298668)D allele alone and jointly with chronic hypertension were associated with a significantly increased risk of preeclampsia
13.3	rs887466 (T;T)

			Source [http://www.nature.com/ng/journal/v38/n10/fig_tab/ng1885_T1.html nature] psoriasis rs887466(G) + rs4379333(C)
13.3	rs1447295 (A;C)	1.7x increased risk of [[prostate cancer]]

			rs1447295 is a SNP on chromosome 8q24, associated with increased risk for prostate cancer in several studies. In a study of over 3,600 Caucasians with prostate cancer, rs1447295 is one of five SNPs used (with family history as a sixth factor) to cumulatively predict overall risk. On their own, the rs1447295(A;A) and (A;C) risk genotypes yield an odds ratio for developing prostate cancer of 1.22 (CI: 1.06-1.40, p=5.3x10-3) and may account for 5.4% of population attributable risk. [http://www.pharmalive.com/News/index.cfm?articleid=428514&categoryid=40] The rs1447295 location could be responsible for about seven percent of prostate cancer cases in white men of north European descent. Thus, taken together with rs6983267, these two genetic changes could account for as much as one quarter of Pr...
13.3	rs4242382 (A;G)	1.7x increased risk for prostate cancer

			rs4242383 is one of 4 tightly linked SNPs in the 'locus 1' region of 8q24 chromosomal region, which has been linked in several studies to prostate cancer, initially through rs1447295. In a study of 1,563 patients of European ancestry, the odds ratio for prostate cancer associated with risk genotypes of locus 1 were reported as 1.70 (CI: 1.39-2.07). Two other regions of chromosome 8q24 were also studied.
13.3	rs131690 (A;A)	normal risk

			rs131690, a SNP in the BCR gene on chromosome 22, has been associated with increased risk for bipolar disorder. The odds ratio for carriers of the minor allele (G) are reported as 1.50 (CI:1.14 - 2.03, p=0.0063) based on a study of 171 Japanese patients.
13.3	rs2713604 (A;G)

			[http://genetics.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pgen.0020139 This paper] implicates this snp as playing a role in heart disease. Having a C at this position is considered normal. Having a T at this position increases the risk of heart disease. Approximate 27% of people carry this risky form.
13.6	rs3825776 (G;G)	>1.3x risk for ALS

			rs3825776, a SNP in the region of the LIPC gene on chromosome 15, has been associated with the sporadic form of ALS (Lou Gehrig's disease) in a study of 1000+ European patients. The odds ratio for the risk allele rs3825776(G) is 1.34 (CI: 1.12 - 1.46).
13.6	rs11964281 (C;T)

			577 African American individuals with T2DM-ESRD and 596 AA controls. *rs11964281 (nominal P = 0.000291, adjusted P = 0.0289)
13.6	rs7451962 (G;G)

			Source [http://www.nature.com/ng/journal/v38/n10/fig_tab/ng1885_T1.html nature] Multiple sclerosis rs9268428(C) + rs6457594(A) + rs7451962(C)
13.6	rs17576 (G;G)	higher risk for lung cancer, and, COPD in smokers; normal risk for MI

			rs17576, also known as Gln279Arg or Q279R, is a SNP in exon 6 of the matrix metalloproteinase-9 MMP9 gene. The rs17576(G) allele encodes the Arg (R). In a study of 385 male veterans with greater than 20 pack-years of cigarette smoking, rs17576(G) allele carriers were at higher risk for chronic obstructive pulmonary disease (COPD). The rs17576(G;G) homozygous genotype was at 3-fold increased risk for COPD. A study of 744 Chinese patients with lung cancer found that the rs17576(G;G) genotype was associated with higher risk of lung cancer with metastasis (adjusted OR, 1.79, CI: 1.03-3.08) compared to the (A;A) genotype. rs17576 is also one of two SNPs in the MMP9 gene associated with increased risk for myocardial infarction, but not coronary artery disease. The relatively weak odds ratios for...
13.8	rs4712653 (C;C)	2x increased risk for neuroblastoma

			SNPs clustered in one region of chromosome 6p22 have been linked to increased risk for the exceedingly rare childhood cancer known as neuroblastoma. A study involving 720 patients determined that rs4712653(C;C) genotypes had increased likelihood of neuroblastoma development (odds ratio 1.96, CI: 1.57 to 2.43, p=7 x 10^-8). At-risk homozygotes diagnosed with neuroblastoma had, on average, more malignant clinical presentation, more aggressive disease, and poorer long-term survival. For more information on this cluster of SNPs, see rs6939340.
15.0	rs6939340 (G;G)	2x increased risk for neuroblastoma

			SNPs clustered in one region of chromosome 6p22 have been linked to increased risk for the exceedingly rare childhood cancer known as neuroblastoma. A study involving 720 patients determined that rs6939340(G;G) genotypes had increased likelihood of neuroblastoma development (odds ratio 1.97, CI: 1.58 to 2.45, p=9.3 x 10^-15). At-risk homozygotes diagnosed with neuroblastoma had, on average, more malignant clinical presentation, more aggressive disease, and poorer long-term survival. Presumably driven primarily by the at-risk homozygotes, the rs6939340(G) allele was considered to be a risk factor, however, there was insufficient data to conclude whether rs6939340(A;G) heterozygotes were actually at any increased risk compared to rs6939340(A;A) 'wild-type' homozygotes. Note that th...
15.0	rs4878104 (T;T)

			linked to Alzheimer's disease
15.0	rs9888739 (C;T)

			[http://content.nejm.org/cgi/content/full/NEJMe0800096 NEJM] a combined analysis of the 7380 independent samples generated a maximum combined P=2.02x1026 and an odds ratio of 1.65 for the association between the T allele of rs9888739 and lupus.
15.0	rs7837688 (G;T)	1.7x increased risk for prostate cancer

			rs7837688 is one of 4 tightly linked SNPs in the 'locus 1' region of 8q24 chromosomal region, which has been linked in several studies to prostate cancer, initially through rs1447295. In a study of 1,563 patients of European ancestry, the odds ratio for prostate cancer associated with risk genotypes of locus 1 were reported as 1.70 (CI: 1.39-2.07). Two other regions of chromosome 8q24 were also studied.
16.7	rs2234693 (C;C)

			rs2234693 is a SNP upstream of the estrogen alpha receptor ESR1 gene, and is sometimes referred to as the -397T>C variation. rs2234693 rs9340799 and rs1256049 variations in ESR1 gene, in addition to the age of a woman, may predict the COH outcome in in vitro fertilization A study of 6,200+ Dutch individuals did not replicate previously reported associations between this SNP (rs2234693) and risk of ischemic stroke rs2234693(C;C)more frequent in African American schizophrenics (p=0.01 to 0.001). haplotype less common in schizophrenia rs2273206(T), rs2273207(G), rs2228480(G).
16.7	rs7017300 (A;C)	1.7x increased risk for prostate cancer

			rs7017300 is one of 4 tightly linked SNPs in the 'locus 1' region of 8q24 chromosomal region, which has been linked in several studies to prostate cancer, initially through rs1447295. In a study of 1,563 patients of European ancestry, the odds ratio for prostate cancer associated with risk genotypes of locus 1 were reported as 1.70 (CI: 1.39-2.07). Two other regions of chromosome 8q24 were also studied.
16.7	rs867186 (A;G)	EPCR H3 haplotype; reduced or increased risk of VTE?

			rs867186 is a SNP that can indicate haplotype H3 of the EPCR gene. The protein product of the EPCR gene activates a part of the anticoagulation pathway. While the rs867186(A) allele could indicate haplotypes H1, H2 or H4, the rs867186(G) allele distinctly tags (identifies) the H3 haplotype. While most groups studying EPCR H3 agree that it leads to increased soluble EPCR, and thus should theoretically lead to reduced risk for venous thromboembolism, different groups come to different conclusions about the effect in the populations each studies. Two find no association [PMID 15304035, PMID 15116250] while one finds that the H3 haplotype (and thus rs867186(G)) actually increases the risk of venous thromboembolism (VTE), with an odds ratio of 1.80, p=0.004.
16.7	rs6133 (G;T)

			[omim:ATOPY, SUSCEPTIBILITY TO]
16.7	rs5082 (C;C)	heavier but lower heart disease risk?
			Individuals homozygous for the -265T>C polymorphism in rs5082, i.e. individuals with the rs5082(C;C) genotype of the Apolipoprotein A-II gene (APOA2) promoter, are associated with increased obesity\|Body Mass Index and food intake in the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) Study.
			rs5082 is a SNP in the apolipoprotein APOA2 gene, and may influence obesity and heart disease risk. Individuals homozygous for the -265T>C polymorphism in rs5082, i.e. individuals with the rs5082(C;C) genotype of the Apolipoprotein A-II gene (APOA2) promoter, are associated with increased obesity\|Body Mass Index and food intake in the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) Study of ~1000 individuals. The odds ratio for obesity in (C;C) individuals compared to rs5082(T) allele carriers was 1.70 (CI: 1.02-2.80, p=0.039). Total energy, total fat, and total protein intake were all significantly higher in (C;C) individuals. In a separate study, a case-control analysis of 484 Australian male coronary artery disease patients concluded that rs5082(C;C) individuals were at signif...
16.7	rs762178 (A;A)

			rs762178 seems to be a potential candidate in altering risk for schizophrenia in the Chinese Han population.
16.7	rs699947 (A;A)	1.36x increased risk for thyroid cancer in men

			The A allele of rs699947 increased a risk for thyroid cancer (adjusted OR=1.36, 95% C.I=1.02~1.81, P=0.039) and regional lymph node metastasis only in men.
16.7	rs7715300 (A;G)

			schizophrenia rs7715300 (p = 0.001) and rs6897690 (p = 0.032)
16.9	rs1540771 (G;G)

			[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000074 plos] the association between rs12203592 and hair color was independent of rs1540771, a SNP between the IRF4 and EXOC2 genes previously found to be associated with hair color.
18.3	rs1061646 (T;T)	normal risk

			breast cancer rs1061646 was associated with risk in the initial study (p=0.0052), and in the replication studies (p=0.032). In a combined analysis, (8,556 cases, 9,605 controls) this SNP yielded an 8% increase in risk per allele. Note that this analysis was carried out in a multi-ethnic study, and rs1061646 showed more consistent association with risk in non-Caucasian populations.
18.3	rs1801280 (C;C)

			rs1801280 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1801280(C).
18.3	rs6983267 (G;G)	1.58x risk for prostate cancer; also colon cancer

			rs6983267 is a SNP on chromosome 8q24, associated with increased risk for prostate cancer in several studies. In studies dividing the 8q24 region, this SNP falls in region 3. In a study of over 3,600 Caucasians with prostate cancer, rs6983267 is one of five SNPs used (with family history as a sixth factor) to cumulatively predict overall risk. On their own, the rs6983267(G;G) and (G;T) risk genotypes yield an odds ratio for developing prostate cancer of 1.37 (CI: 1.18-1.59, p=3.4-10e-5) and may account for 22.2% of population attributable risk. The increased risk of developing prostate cancer associated with rs6983267 now appears to be independent of the risk associated with it's close neighbor, rs1447295. The odds ratio for heterozygotes is estimated to be 1.26 (CI: 1.13 - 1.41), and for ...
18.3	rs998075 (C;C)

			related IGF2R Ex16+88G>A rs998075 alters methylation affecting osteosarcoma
18.3	rs1208 (G;G)

			rs1208 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1208(G).
20.0	rs9217 (G;G)

			Variations in this snp have been linked to nicotine dependence [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16874522&query_hl=3&itool=pubmed_docsum]
20.0	rs1343151 (T;T)	0.8x lower risk for spondylitis

			rs1343151 is one of several SNPs in the IL23R gene that has been shown in a large (over 1,000 Caucasian patients) study to be associated with ankylosing spondylitis. The odds ratio is 0.8 (p=1.0x10e-5).[PMID 17952073, PMID 18037607]
20.0	rs1990760 (C;T)

			[http://jcem.endojournals.org/cgi/content/abstract/92/8/3338 Abstract] associated with type-1 diabetes, organ-specific autoimmune diseases, including Graves' disease. (odds ratio 1.47 (CI: 1.231.76, p = 1.9 x 10⁵) This polymorphism may also contribute to several other autoimmune disorders. A study of 261 Chinese patients with Graves' disease failed to find any association with rs1990760.
20.0	rs6469792 (C;C)

			[http://www.medpagetoday.com/Endocrinology/Osteoporosis/tb/9271 news] rs6469792 and rs6469804 association with bone mineral density.
20.0	rs17602729 (A;G)	AMPD1 heterozygote

			rs17602729, a SNP located in the AMPD1 gene and also known as 'C34T', has at times been called the 'most prevalent genetic disease mutation', at least in Caucasians. Perhaps up to 10% of Caucasians and African-American carry one C34T allele (i.e. carry one rs17602729(A) allele) - and actually, most of them are unaware of any medically related issues since they don't typically have any particular symptoms that would warrant a trip to the doctor. So what's the issue? The AMPD1 gene encodes the enzyme adenosine monophosphate deaminase, which is one of the key enzymes used to process the energy source ATP. The C34T variation causes a premature stop in the protein, leading to a nonfunctional AMPD1 enzyme. Some individuals - but by no means all or even a majority apparently - who are AMPD1 defi...
20.3	rs7757037 (A;A)	0.63x decreased risk for bipolar disorder

			rs7757037, a SNP in the FKBP5 gene, is associated with increased risk for bipolar disorder in a study of 500+ Caucasian patients. The most common allele, rs7757037(G), was associated with highest risk. Giving that allele a relative odds ratio of 1.0, the odds for the (A;G) and (A;A) genotypes were 0.68x (CI:0.53-0.87, p=0.007) and 0.63x (CI: 0.45-0.89, p=0.007).
20.3	rs6457617 (T;T)	5.2x risk

			rs6457617 has been reported in a large study to be associated with rheumatoid arthritis. This SNP is reported to be the most statistically significant of many SNPs similarly located in the MHC region. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated with heterozygotes is 2.36 (CI 1.97-2.84), and for homozygotes, 5.21 (CI 4.31-6.30).
20.7	rs2280089 (A;G)

			rs2280089, a SNP in the ADAM33 gene, has been linked to a predisposition to asthma and bronchial hyperresponsiveness. [PMID 12110844, PMID 14564349]
20.7	rs3024496 (T;T)

			Dust mite exposure modifies the effect of functional IL10 polymorphisms on allergy and asthma exacerbations. Dust mite exposure significantly modified the relation between 3 SNPs in IL10 (rs1800896, rs3024492, and rs3024496). Homozygosity for the minor allele of each of the 3 SNPs was associated with increased risk of occurrence ( approximately 3-fold to 39-fold increase)
21.7	rs5051 (C;C)	normal risk

			rs5051 is a SNP in the promoter of the angiotensin AGT gene, and presumably due to it's tight linkage with rs699, the rs5051(T) allele - as oriented to the dbSNP entry, not as published - has been associated with increased risk for hypertension and complications thereof. rs699(T) is associated with higher plasma angiotensinogen levels, and therefore the increased risk of essential hypertension. The frequency of the rs699(T) allele is also generally higher in African populations compared to Caucasian populations, correlating to the higher incidence of hypertension in African population. rs5051 is also known as 'A-6G'. For more details, see rs699. rs5051(T;T) homozygotes have been reported to be at increased risk for Crohn's disease, as based on one cohort of ~350 Australian patients. The od...
21.7	rs2303067 (A;A)	1.8x risk

			rs2303067, a SNP in the SPINK5 gene, has been significantly associated with susceptibility to atopic dermatitis. The risk allele for rs2303067 is (A). rs2303067 has also been associated with predisposition to asthma, . From this study: 'A significant association between rs2303067 and the development of asthma was observed (OR 1.77; 95%CI: 1.02-3.06, P=0.041 for rs2303067(A;A) homozygotes). Atopic carriers of rs2303067 showed an increased risk for asthma and asthma symptoms (OR 2.06; 95%CI: 1.01-4.20, P=0.047). When children with a combination of asthma and atopic dermatitis were compared with normal controls, the rs2303067(A) genotype was more prevalent in the disease group (OR 4.56; 95%CI: 1.370-15.12, P=0.007).'
21.7	rs1800896 (A;A)

			Dust mite exposure modifies the effect of functional IL10 polymorphisms on allergy and asthma exacerbations. Dust mite exposure significantly modified the relation between 3 SNPs in IL10 (rs1800896, rs3024492, and rs3024496). Homozygosity for the minor allele of each of the 3 SNPs was associated with increased risk of occurrence ( approximately 3-fold to 39-fold increase)
21.7	rs17822931 (C;T)	wet earwax

			This SNP determines wet vs dry earwax as well as sweat production it is commonly (T;T) for asians and (C;C) for europeans and africans.
21.7	rs2236225 (T;T)

			[omim:NEURAL TUBE DEFECTS, FOLATE-SENSITIVE, SUSCEPTIBILITY TO]
21.7	rs5945572 (G;G)

			Associated with prostate cancer
21.7	rs17137124 (T;T)

			variations in rs17137124 and rs10227893 may impair speech
21.7	rs534654 (C;T)

			Along with rs6442925 and rs1534891, this SNP, rs534654, is part of a 3-SNP (multi-locus) interaction that is associated with bipolar disorder.
21.7	rs10116277 (T;T)

			discussed in this [http://suicyte.wordpress.com/2007/05/26/soul-searching-i/ blog post] A region of chromosome 9p21 has revealed numerous SNPs correlated with risk of myocardial infarction in a study of 2,000+ patients. This SNP, rs10116277, is highly correlated (r²=0.9) with rs2383207, as well as rs1333040 (r²=0.67). Ultimately, though, the SNP in this study (and region) with the highest disease correlation is rs10757278.
21.7	rs3741208 (T;T)

			associated with type-1 diabetes
21.7	rs11574637 (C;T)

			Associated with systemic lupus erythematosus (SLE)
22.0	rs140504 (A;G)	1.4x increased risk for bipolar disorder

			rs140504, a SNP in the BCR gene on chromosome 22, has been associated with increased risk for bipolar disorder. The odds ratio for carriers of the minor allele (G) are reported as 1.45 (CI:1.11 - 1.84, p=0.0054) based on a study of 171 Japanese patients.
22.4	rs2518136 (C;C)

			Associated with type-2 diabetes in a study of Danish (but apparently not Swedish or French) Caucasians
23.3	rs4825476 (A;A)	normal

			This SNP, located in an intron of the GRIA3 gene (also known as AMPA3), has been linked in one study to increased thoughts of suicide in patients taking the anti-depressant drug citalopram. The increased risk is calculated to be 1.9x. If the individual is also carrying two rs2518224(C) alleles, i.e. is a rs2518224(C;C) homozygote, the odds ratio for having suicidal thoughts is increased to ~15x (CI: 3.7 - 60.6).
23.3	rs2040639 (G;G)

			18067C>T possibly related to non-Hodgkin lymphoma rs2040639-AG, contribute to oral cancer risk. pseudo-haplotype with AG-CC genotypes in 2.45x risk rs2040639-rs861539 5.03x risk rs2040639-rs861539-rs2075685 *10.10x risk rs2040639-rs861539-rs2075685-rs1799782
23.3	rs7903146 (C;C)	normal form

			This SNP in TCF7L2 influences the risk of Type-2 diabetes (T2D). rs7903146(C;T) rs7903146(T;T) strongly predicted future type-2 diabetes. Considered in context with rs7903146 rs12255372 rs10885406. Note: this is one of two SNPs within the TCF7L2 gene that have been reported to be associated with type-2 diabetes, the other being rs4506565. They have approximately equal power to estimate risk for type-2 diabetes, and the results from one correlate 92% of the time with the other. [http://medicine.plosjournals.org/perlserv/request=get-documentamp?request=get-document&doi=10.1371/journal.pmed.0030374 Full text of the paper] is available from from Plos Medicine. Or from NCBI as . TCF7L2 polymorphisms and progression to diabetes in the Diabetes Prevention Program. reconfirmed in a diverse pop...
23.3	rs2383207 (G;G)	increased risk for heart disease

			discussed in this [http://suicyte.wordpress.com/2007/05/26/soul-searching-i/ blog post] as possibly playing a role in coronary heart disease This SNP was also associated with increased risk for coronary artery disease in a Korean population. The association remained significant after adjusting for significant clinical covariates (P=0.001 to 0.024). We identified one risk haplotype (GGGG; P=0.017) and one protective haplotype (AAAA; P=0.007) for development of CAD. Further analysis suggested that the SNPs probably confer susceptibility to CAD in a dominance model (covariates-adjusted P=0.001 to 0.024; OR=2.37 to 1.54). Also found to be significant in a study of 416 Italian myocardial infarction patients.
23.3	rs2228480 (A;G)

			haplotype less common in schizophrenia rs2273206(T), rs2273207(G), rs2228480(G).
23.3	rs509749 (A;A)	common; slight increase in SLE risk

			rs509749 is a SNP in exon 8 of the LY9 gene; this SNP is also known as Met602Val. The (A) allele encodes the Met; the (G) allele encodes the Val. The rarer (G) allele is undertransmitted in a family-based association study of systemic lupus erythematosus, leading to the conclusion that the (A) allele increases risk for SLE by increasing cytokine production and thereby enhancing the immune response.
25.0	rs6469804 (A;A)

			[http://www.medpagetoday.com/Endocrinology/Osteoporosis/tb/9271 news] rs6469792 and rs6469804 association with bone mineral density.
25.0	rs6675281 (C;T)

			linked to schizophrenia
25.0	rs2239518 (C;T)

			schizophrenia the SNPs (rs1049623, rs2267641 and rs2239518) haplotype remaining significant even after adjustment for multiple testing (adjusted P=0.0136).
25.0	rs4680 (A;A)	multiple associations, see details

			rs4680 is a well studied SNP in the catechol-O-methyltransferase COMT gene. rs4680 is also known as the Val158Met polymorphism; note that rs4680(G) encodes the Val, considered to be the high enzymatic activity form, and rs4680(A) encodes the Met (lower enzymatic activity). Part of a three-marker haplotype rs737865-rs4680-rs165599 rs4680, a functional Val/Met polymorphism, showed modest association with Irish familial schizophrenia. Haplotype A-G-A for SNPs rs737865-rs4680-rs165599 was preferentially transmitted to the affected subjects. A study of 400 individuals reported that an increase in plasma total homocysteine (tHcy) of 10.4% (CI: 0.01-0.21, p=0.03) for associated with rs4680(A;A) homozygotes compared with rs4680(G;G) subjects. The (A;A) genotype was also more common, but statistica...
25.0	rs688 (T;T)	1.5x higher risk for males of Alzheimer's

			RNA made containing the rs688(T) SNP, a variant near exon 12 of the low-density lipoprotein receptor (LDLR) that is a receptor for ApoE proteins, is spliced at lower efficiency in males. Presumably due to this, the rs688(T;T) genotype was associated with increased risk for Alzheimer's disease odds in males (odds ratio 1.49, CI: 1.13-1.97, uncorrected p=0.005), but not in females.
25.0	rs2016520 (A;A)

			Associated with baseline cholesterol levels in a study of 9,000+ individuals in Washington County, Maryland.
25.0	rs279858 (A;A)

			This SNP in the GABRA2 gene has been linked to Alcoholism. The effect of this SNP, a synonymous change at amino acid residue 132, is unknown, but it does not change the GABRA2 protein sequence. Carriers of at least one rs279858(G) allele respond slower to the effects of alcohol and are thereby apparently more prone to alcoholism than carriers of two rs279858(A) alleles. Finasteride, an FDA approved drug for the treatment of benign prostatic hypertrophy and a modulator of GABRA2, was shown to have more of a blocking effect on rs279858(A) homozygotes. Note that nearby SNPs have been grouped into a haplotype that shows statistically stronger association with alcohol dependence, namely the haplotype consisting of the rs279871(A) + rs279845(T) + rs279836(A) alleles .
25.0	rs931127 (A;A)	2.15x more likely positive lymph node
			[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16563182 PMID: 16563182] In women diagnosed with breast cancer, this genotype less favorable. It is more associated with lymph node metastasis than (G;G). The study found that 33.3% of those with GG genotype had positive lymph nodes as compared with 52.7% among those with GA or AA genotype (P = 0.0139). An individual with the GA or AA genotype was 2.15 times more likely to have positive lymph nodes than was an individual with GG genotype.
			[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16563182&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum PMID: 16563182 ] This SNP in can have implications for prognosis in breast cancer. It is located 313 base pairs upstream of the 5'-untranslated region of SIPA1 and is considered to be within the promoter region of the gene. SIPA1 germline polymorphisms are associated with aggressive disease behavior(lymph node metastasis) in the cohort examined
25.9	rs20417 (C;G)	normal risk of diabetes

			In a group of Pima Indians, individuals with the variant PTGS2 rs20417 CC genotype had a 30% higher Type 2 diabetes prevalence compared with subjects with the GG genotype
25.9	rs7528684 (A;A)	normal

			rs7528684 rs3792876 and rs2268277 failed to showed a statistically significant association with rheumatoid arthritis rs7528684 has been reported to be associated with rheumatoid arthritis in a Caucasian population, following reports of a similar association in a Japanese population. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 0.95 (CI 0.83-1.08), and for homozygotes, 2.30 (CI 1.64-3.23). In a study of 645 Caucasians from Southern Spain with multiple sclerosis, the rs7528684(G) allele (in dbSNP orientation) was found to be somewhat protective (per allele odds ratio 0.81, CI: 0.70-0.94, p=0.007). In another report , a summary indicates the following regarding disease and odds ratio (OR)for rs7528684: * for rheumatoid arthritis: OR =...
26.3	rs11571316 (C;C)

			associated with type-1 diabetes
26.7	rs761100 (G;G)	higher risk for dyslexia

			The more common allele of rs761100 has been linked to increased risk for developmental dyslexia in a study of ~300 British families. While odds ratios were not reported, the significance was reported as p=0.02.
26.7	rs4939827 (T;T)	1x normal risk for colorectal cancer

			rs4939827 is one of 3 SNPs in the SMAD7 gene associated with risk for colorectal cancer, based on a large study (7,400+ cases) conducted in the UK. The odds ratios show a decreased risk for the minor rs4939827(C) allele; the OR for (C;C) homozygotes is 0.73 (CI: 0.66-0.8), and for (C;T) heterozygotes 0.86 (CI: 0.79-0.92), overall p=1x10^-12.
26.7	rs1554973 (C;T)

			In the study the researchers analysed DNA from placental tissue samples and cord blood from 111 women and their babies and found that maternal rs1079932) and one foetal rs1554973 demonstrated highly significant association with chorionic plate inflammation. [http://www.thaindian.com/newsportal/health/genetic-mutation-behind-increased-preterm-birth-risk_10015965.html news]
26.7	rs5065 (A;G)	normal risk

			rs5065, also known as T2238C, is a SNP in the atrial natriuretic precursor A NPPA gene. A large study has been conducted in which 42,418 hypertensive participants 55 or older were followed for several years while on one of four medications: a diuretic, a calcium antagonist, an angiotensin-converting enzyme inhibitor, or an alpha-blocker. The primary endpoint was either fatal heart disease or a heart attack. The blood pressure after six months of rs5065(G;G) patients (note: genotype is in dbSNP orientation, not as published) was lower if the patients were treated with diuretics compared to other medications, with smaller variation seen for (A;A) genotypes. The authors noted that none of the findings retained statistical significance after correction for multiple comparisons, but since the t...
26.7	rs6601764 (T;T)	normal

			rs6601764 has been reported in a large study to be associated with Crohn's disease. The risk allele (oriented to the dbSNP entry) is (C); the odds ratio associated with heterozygotes is 1.16 (CI 1.01-1.33), and for homozygotes, 1.52 (CI 1.28-1.80).
26.7	rs5443 (C;C)	average

			rs5443, a SNP in the G-protein beta3 subunit (GNB3) gene that is more commonly known as the C825T variant, has been linked to a number of metabolic conditions including obesity, coronary artery disease, insulin resistance and therefore diabetes, left ventricular hypertrophy, and hypertension. It has also been linked to how well a patient responds to Viagra (sildenafil). Several studies have been unable to replicate one or more of the associations in at least some populations between this SNP and these conditions. The more notable studies include: rs5443(T) allele carriers are 2-3 fold more likely to be obese in Caucasian, Chinese, and African American populations. rs5443(T) carriers are clearly at higher risk for hypertension, but this review indicates that whether they are also at incr...
26.7	rs4633 (T;T)	higher risk for endometrial cancer

			rs4633 is a variant at codon 62 of the COMT gene, however, it does not change the amino acid sequence of the COMT protein. In a study of 150 (Caucasian) cases of endometrial cancer, a significant increase in rs4633(T;T) genotype was observed in patients compared to controls (OR = 2.39, CI: 1.31-4.37, p = 0.004). Furthemore, the frequency of the C-G haplotype of rs4633-rs4680 was significantly higher in controls (p < 0.0001) than in patients. This correlated with lower expression levels of the COMT protein in carriers of these alleles. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1180576 pubmed 1180576] Schizophrenia Susceptibility Genetic basis for individual variations in pain perception and the development of a chronic pain condition
26.7	rs7574865 (G;T)	1.3x risk for RA; 1.5x for SLE

			rs7574865, a SNP in the third intron of the STAT4 gene, has been reported in a large study of Swedes to be associated with both rheumatoid arthritis and lupus (SLE). The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated the presence of a risk allele was 1.3 for rheumatoid arthritis and 1.55 for lupus (SLE). The paper states that, 'Homozygosity of the risk allele, as compared with absence of the allele, was associated with a more than doubled risk for lupus and a 60% increased risk for rheumatoid arthritis.' A study of 124 Caucasian patients with primary Sjogren's syndrome, a related autoimmune disease to RA and SLE, also found that the rs7574865(T) allele to be associated with higher risk for this condition (p=0.01).
26.7	rs3761847 (G;G)	>1.3x risk

			rs3761847, a SNP located between two genes associated with chronic inflammation (TRAF1 and C5), is associated with increased risk of antiCCP-positive rheumatoid arthritis. The risk allele is (G); the odds ratio reported is 1.32 (95% confidence interval, 1.23 to 1.42; P=4x1014) .
26.7	rs4355801 (A;A)

			[http://www.medpagetoday.com/Endocrinology/Osteoporosis/tb/9271 news] rs4355801, was associated with a 20% increased risk of osteoporosis (significant at P=0.038). At least one copy of the risk allele of rs4355801 was found in 79% of study participants. Participants carrying at least one copy of each risk allele -- 22% of the study population -- had a 50% increased risk of osteoporosis, which was significant at P=0.0026, and a 29% increased risk of osteoporotic fractures (significant at P=0.014). rs3736228 associated with decreased bone mineral density (p=6.3x10(-12) for lumbar spine and p=1.9x10(-4) for femoral neck) and an increased risk of both osteoporotic fractures (odds ratio [OR] 1.3, 95% CI 1.09-1.52, p=0.002) and osteoporosis (OR 1.3, 1.08-1.63, p=0.008). rs4355801 associated with...
27.1	rs2710102 (T;T)

			rs2710102, a common SNP in the CNTNAP2 gene, was found to be significantly associated (p<0.028) with a delayed onset of speech, as measured by the age at which a child speaks their first words, in children with autism. This effect is primarily seen in males, perhaps correlated with the 4-5x overrepresentation of males with autism compared with females. The confirmatory Stage 2 study was performed on 304 independent parent-child trios. However, the risk allele and the degree to which speech is delayed per genotype is unclear as published and awaits clarification by the authors.
28.3	rs1800797 (G;G)

			rs1800797, rs1800796 and rs1800795 have been shown to affect both the transcription and secretion of IL-6, to symptomatic distal interphalangeal osteoarthritis based on 535 women. the G alleles of two promoter single-nucleotide polymorphisms (SNP) G-597A and G-174C were more common among the subjects with symptomatic DIP OA than among those with no disease (p-values corrected for multiple testing 0.020 and 0.024). Also, the carriage of at least one G allele in these positions increased the risk of disease (p=0.006 and, p=0.008, respectively). Carrying a haplotype with the G allele in all three promoter SNPs increased the risk of symptomatic DIP OA more than four-fold (OR 4.45, p=0.001). Carriage of the G-G diplotype indicated an increased risk of both symmetrical DIP OA (OR 1.52 95% CI 1.0...
28.3	rs1893217 (C;T)

			linked to Crohn's disease and type-1 diabetes
28.3	rs1137101 (G;G)

			[omim:LEPTIN RECEPTOR POLYMORPHISM]
28.3	rs2143340 (C;T)	increased risk

			Rs2143340, a SNP in the TTRAP gene, is in a region that crops up in several independent studies as likely to associated with dyslexia. The risk allele in the US/UK Caucasian populations studied is (C), and it is indicative of a risk haplotype found in ~18% of the general population but up to ~28% of severely dyslexic individuals. It is not thought that rs2143340 is a functional SNP; instead, it marks the haplotype known as rs4504469-rs2038137-rs2143340 '1-1-2' since the other two SNPs are the common forms whereas the significant form for rs2143340 is the rare form. The functional effect of this haplotype appears to be on the KIAA0319 gene, in that KIAA0319 gene activity associated with the 1-1-2 risk haplotype is 40% lower than for other haplotypes, and other genes aren't noticeably affec...
28.3	rs1800321 (A;A)

			[omim:ORNITHINE TRANSCARBAMYLASE POLYMORPHISM]
28.3	rs13036957 (A;G)

			This SNP was associated with amyotrophic lateral sclerosis (ALS) based on a study of 1,152 patients.
28.3	rs7076156 (A;G)

			[omim:URIC ACID NEPHROLITHIASIS, SUSCEPTIBILITY TO]
28.3	rs1800630 (A;C)	1.8x increased lupus risk

			rs1800630 is a SNP upstream of the tumor necrosis alpha (TNF) gene; this SNP is also typically called the -863 variant. In a study of 154 Thai patients with systemic lupus erythematosus (SLE), rs1800630(A) allele frequency was significantly increased, with an odds ratio of 1.85 (CI: 1.21-2.83, p(corr) = 0.009). This allele was also found to be significantly increased in the SLE group with Raynaud's phenomenon compared to SLE without Raynaud's phenomenon ( odds ratio of 2.23, CI: 1.21-4.10, p(corr) = 0.048).
28.3	rs6280 (C;T)	normal

			rs6280 is a SNP in the dopamine receptor D3 DRD3 gene. The rs6280(C) allele encodes a glycine, and the (T) allele encodes a serine (in dbSNP orientation). In a study of 88 patients being treated for schizophrenia with olanzapine, those who were rs6280(C;C) homozygotes had greater positive symptom remission (endpoint rating of minimal or none on all PANSS clinical response positive items, 39.1%), as compared with (C;T) or (T;T) genotypes (13.8%; p = 0.033).
28.3	rs5215 (T;T)

			The association between type-1 diabetes and rs5215 is mentioned as being replicated in ; there is also a 90% correlation between rs5215 and rs5219.
28.3	rs709932 (A;G)

			[omim:PI M4]
28.3	rs1042838 (G;T)	1.26x risk for ovarian cancer

			Two SNPs in haplotype block 4 of the PGR gene were associated with an increased risk of ovarian cancer among homozygous carriers as compared with noncarriers: rs1042838 (PROGINS allele; odds ratio [OR] = 3.23, 95% confidence interval [CI] = 1.19 to 8.75, P = .022) and rs608995 (minor allele; OR = 3.10, 95% CI = 1.63 to 5.89, P<.001). For rs1042838, the risk allele in orientation to the corresponding dbSNP entry is (T). This SNP, which is located in the progesterone receptor gene PGR, has also been reported to be associated with migraine-associated vertigo. SNPs in genes involved in female hormonal pathways have been a subject of particular interest in the study of migraines because females appear to be more prone to migraines than males.
28.3	rs2241880 (C;C)	2x risk

			rs2241880, a SNP in the ATG16L1 gene encoding a threonine to alanine substitution ('T300A') in a protein known to be involved in the function of the epithelial cells lining the intestine, has been associated with Crohn's disease in several recent studies. [PMID 17200669, PMID 17435756] In another recent (2007) report, rs2241880 is confirmed to be associated with both Crohn's disease and ileal disease, but additionally, the authors calculate risk for individuals who are homozygotes for this SNP plus 2 others (in the IBD5 and NOD2 genes). Individuals homozygous for the risk alleles for all 3 of these SNPs are estimated to be at 20 fold higher risk (CI ~9-49) for Crohn's disease. From the largest most recent survey, the Crohn's disease-associated SNPs for IBD5 and NOD2 are, respectively, rs6...
28.3	rs3750344 (A;G)

			Is Associated with Nicotine Dependence
28.8	rs11052552 (G;G)	1.4x risk

			rs11052552 has been reported in a large study to be associated with type-1 diabetes. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.49 (CI 1.28-1.73), and for homozygotes, 1.43 (CI 1.21-1.69).
30.0	rs9900972 (A;G)

			rs6996321 significantly related to spine bone mineral density (p=0.002) and rs10914367 associated with hip BMD (p=0.028). Non-vertebral fracture risk was significantly increased in carriers of 'A' allele of rs9900972 (OR=2.06, p=0.0187)
30.0	rs9786043 (T;T)
			[haplogroup:K-R]
			[haplogroup:?]
30.0	rs12255372 (G;T)	?
			This is the genotype of User:Watson
			This SNP is in the TCF7L2 gene, and has been linked to type-2 diabetes, breast cancer and aggressive prostate cancer. is the paper which links it to Breast cancer. It suggests the T allele as increasing risk. reports the association of rs12255372 and rs7903146 with Type-2 diabetes in a Finnish sample. rs12255372 Common variants (rs12255372 and rs7903146) in TCF7L2 seem to be associated with an increased risk of diabetes among persons with impaired glucose tolerance Considered for type-2 diabetes with rs7903146 rs12255372 rs10885406. Associated in a study of ~1000 Hispanic-Americans with reduced insulin secretion as measured by acute insulin response and adjusted for the degree of insulin sensitivity (p = 0.036). In a study of 1,457 prostate cancer cases and 1,351 controls, while there w...
30.0	rs10489629 (G;G)	0.83x lower risk for spondylitis

			rs10489629 is one of several SNPs in the IL23R gene that has been shown in a large (over 1,000 Caucasian patients) study to be associated with ankylosing spondylitis. The odds ratio is 0.83 (p=0.00014).[PMID 17952073, PMID 18037607]
30.0	rs27072 (C;T)	normal

			rs27072, a SNP in the dopamine transporter SLC6A3 gene, has been associated with more severe symptoms upon alcohol withdrawal, such as seizures, in a study of 250 Caucasian alcohol-dependent patients. Two haplotypes appear to be tagged by this SNP and a neighbor, rs27048.
30.0	rs1130866 (T;T)	if sclerotic, reduced risk of lung disease

			rs1130866 is a SNP altering an amino acid at position 131 of the pulmonary-associated protein B surfactant SFTPB gene. On it's own, it does not affect the odds of acquiring systemic sclerosis. However, in a study of 127 Japanese patients who already had systemic sclerosis, rs1130866(T;T) homozygotes were found to be at reduced risk for interstitial lung disease.
30.0	rs17315821 (T;T)

			[haplogroup:?]
30.0	rs27048 (C;C)	2x risk of severe alcohol withdrawal

			rs27048, a SNP in the dopamine transporter SLC6A3 gene, has been associated with more severe symptoms upon alcohol withdrawal, such as seizures, in a study of 250 Caucasian alcohol-dependent patients. Two haplotypes appear to be tagged by this SNP and a neighbor, rs27072.
30.0	rs9786119 (G;G)
			[haplogroup:P]
			[haplogroup:?]
30.0	rs9786896 (G;G)
			[haplogroup:P]
			[haplogroup:?]
30.0	rs363050 (G;G)	normal IQ

			This is one of four SNPs in the first intron of the SNAP25 gene that have been correlated with increased intelligence based on studies of ~300 Caucasian subjects. The (A;A) genotype averages 2.84 PIQ points higher than the (A;G) genotype, which averages 2.8 PIQ points higher than the (G;G) genotype (p=0.0002). Variance in this SNP may account for 3.4% of the phenotypic variance in PIQ. rs363050 is in close linkage with rs353016, with r2 = 0.98, such that the rs363050(A) allele typically is linked to the rs353016(T) allele. For SNPs rs363039 - rs363043 - rs353016, respectively, the haplotype C-T-T is most associated with higher intelligence in children, whereas the haplotype C-C-T is most associated in adults (SNPs oriented as in dbSNP).
30.0	rs3748079 (A;G)	normal risk

			rs3748079 is a SNP in the promoter region of the ITPR3 gene; it is also known as -1990C>T. rs3748079 has been linked to increased risk for systemic lupus erythematosus (SLE) in two independent Japanese case-control samples (p=0.0000000178 with odds ratio of 1.88, CI:1.51-2.35). Individuals with risk genotypes of both rs3748079 and rs3095870, in the ITPR3 and NKX2.5 genes, respectively, have even high risk for SLE (odds ratio 5.77). This particular SNP also revealed associations with rheumatoid arthritis (RA) (p=0.0084 with odds ratio of 1.23, CI:1.05-1.43) and with Graves' disease (GD) (p=0.00036 with odds ratio of 1.57, CI:1.22-2.02). Note that the orientation of this SNP as published is reversed compared to the dbSNP entry.
30.0	rs895530 (G;G)
			[haplogroup:P]
			[haplogroup:?]
30.0	rs363039 (C;C)	higher IQ

			This is one of four SNPs in the first intron of the SNAP25 gene that have been correlated with increased intelligence based on studies of ~300 Caucasian subjects. In orientation to the dbSNP entry for this SNP, rather than as published, the (C;C) genotype averages ~2 PIQ points higher than the (C;T) genotype, which averages 2 PIQ points higher than the (T;T) genotype. For SNPs rs363039 - rs363043 - rs353016, respectively, the haplotype C-T-T is most associated with higher intelligence in children, whereas the haplotype C-C-T is most associated in adults (SNPs oriented as in dbSNP).
31.7	rs251124 (C;T)

			http://stroke.ahajournals.org/cgi/reprint/37/9/2372 rs251124 (OR1.43, 95% CI1.09 to 1.88, P0.008) and rs173686 (OR1.34; 95% CI1.09 to 1.65, P0.004) linked to increased risk for disruption of the extracellular matrix (ECM) of the arterial wall and is a likely factor in the pathogenesis of intracranial aneurysms (IAs).
31.7	rs838552 (C;T)

			linked to late onset Parkinson's disease
31.7	rs1333040 (T;T)

			discussed in this [http://suicyte.wordpress.com/2007/05/26/soul-searching-i/ blog post]
31.7	rs2227564 (C;T)

			rs2227564 A functional polymorphism within plasminogen activator urokinase (PLAU) is associated with Alzheimer's disease . *rs2227564 distribution of four tagSNPs (rs2227562 in intron 5, rs2227564 in exon 6, rs2227571 in intron 9, and rs4065 in 3'UTR) in the PLAU gene in a large case-control study of Alzheimer's disease [omim:ALZHEIMER DISEASE, LATE-ONSET, SUSCEPTIBILITY TO]
31.7	rs663048 (G;T)

			rs663048 associated with lung cancer The homozygotes for the variant allele had more than a 3-fold risk compared with the wild-type homozygotes [combined odds ratio (OR), 3.32; 95% confidence interval (95% CI), 1.81-7.21]. Heterozygotes also had a significantly elevated risk of lung cancer from the combined replication studies with an OR of 1.15 (95% CI, 1.04-1.59). The effect remained significant after adjusting for age, gender, and pack-years of tobacco smoke.007;67(17):8406-11].
31.7	rs2076530 (A;A)	2x risk for sarcoidosis

			rs2076530(A) was estimated to double the risk of developing sarcoidosis, at least as based on a study of Caucasians. Although by itself it was not associated with increased risk for sarcoidosis in a population of African descent, this allele was part of a disease-associated haplotype. The rs2076530 SNP has also been investigated for associations with multiple sclerosis, Type-1 diabetes, SLE, and rheumatoid arthritis, but any association seen has apparently been due to carryover effects from nearby major histocompatibility haplotypes. [PMID 16690410, PMID 16321988]
31.7	rs486907 (G;G)

			[omim:PROSTATE CANCER, SUSCEPTIBILITY TO]
31.7	rs135551 (C;T)

			667 cases and 862 controls (OR=0.87, P=0.046, 95% CI=0.72-0.99 for rs135551; OR=0.80, P=0.034, 95% myocardial infarction in a European population.
31.7	rs251177 (C;T)	somewhat higher risk for prostate cancer

			rs251177 is one of seven SNPs found in a combined study of over 1,000 patients to be associated with increased risk for prostate cancer. The risk allele for this SNP is (C); and while the odds ratio was not specifically reported, the probability of false significance (not permuted though) was given as p=0.000188, using an additive model of risk.
31.7	rs213950 (G;G)	normal

			rs213950, a SNP in the cystic fibrosis CFTR gene, has been reported in a large study to be associated with type-1 diabetes. In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for this SNP was recalculated to be 1.09 (CI 1.041.15). [omim:CFTR POLYMORPHISM]
32.2	rs788016 (A;A)

			G-C-T-C haplotype of rs2340690-rs788016-rs2305560-rs2565163 has odds ratio of 1.91 (CI: 1.26-2.89, p=0.002) for coronary heart disease compared to G-T-T-C, based on a study of 1,000 Han Chinese patients and matched controls. * Note: Haplotype allele assignments may not be in dbSNP orientation.
33.3	rs2281845 (G;G)

			[omim:THYROTOXIC PERIODIC PARALYSIS, SUSCEPTIBILITY TO]
33.3	rs11650354 (C;T)	possible risk for allergic asthma

			A large study of Caucasian children has identified this SNP in the TBX21 gene (and one other, rs16947078) as defining a haplotype associated with increased risk for allergic asthma. The odds ratio associated with rs11650354(T;T) homozygotes compared to rs11650354(C;C) homozygotes for allergic asthma is reported to be 8.13 (CI: 2.5-26.9). Heterozygotes may be at slightly higher risk.
33.3	rs10504543 (G;G)

			Left ventricle systolic dimension, rs10504543 (KCNB2, p = 5.18*10(-6))
33.3	rs885834 (A;A)

			associated with specific patterns of brain activity. rs3087454 rs1355920 rs7520974 rs885834
33.3	rs4713902 (C;T)	0.69x decreased risk for bipolar disorder

			rs4713902, a SNP in the FKBP5 gene, is associated with increased risk for bipolar disorder in a study of 500+ Caucasian patients. The most common allele, rs4713902(T), was associated with highest risk. Giving that allele a relative odds ratio of 1.0, the odds for the (C;T) and (C;C) genotypes were 0.69x (CI:0.55-0.88, p=0.001) and 0.47 (CI: 0.30-0.74, p=0.001).
33.3	rs2881766 (G;T)	increased risk for pregnancy-induced hypertension

			rs2881766 is a SNP in the promoter region of the estrogen receptor alpha ESR1 gene. Carriers of rs2881766(T) alleles are at somewhat (slightly) higher risk for pregnancy-induced hypertension.
33.3	rs2660899 (G;T)

			Despite earlier reports of an association, no risk for myocardial infarction was seen for rs2660899 variants in a study of 1,211 German patients.
33.9	rs1801133 (C;T)	multiple, incl 1.17x for gastric cancer

			rs1801133 is a SNP that is relatively common and has been studied for (relatively) a long time. Also known as C677CT, Ala222Val, and A222V, it encodes a variant in the MTHFR gene, which encodes an enzyme involved in folate metabolism. Homozygous rs1801133(T;T) individuals have ~30% of the expected MTHFR enzyme activity, and rs1801133(C;T) heterozygotes have ~65% activity, compared to the most common genotype, rs1801133(C;C). This reduced activity (i.e. this SNP) has been linked at least once to each of the following disorders (though not necessarily reproducibly): coronary artery disease neural tube defects migraine thrombosis preeclampsia cleft lip/palate autism depression schizophrenia cancer, including **gastric cancer With regard to gastric cancer, a meta-analysis combining 1...
35.0	rs1801260 (C;T)

			rs1801260, a SNP in the CLOCK gene known as 3111 T/C, has been reported to influence sleep and activity patterns in patients affected by bipolar depression. From this article's abstract: 'Compared to T/T homozygotes, carriers of the C allele had a similar degree of severity of depression, but showed higher activity levels in the evening, a delayed sleep onset (mean 79 min later), and a reduced amount of sleep during the night (mean 75 min less).'
35.0	rs1695 (A;A)	normal

			This snp, in the GSTP1 gene influences asthma risk mentioned in this [http://news.bbc.co.uk/2/hi/uk_news/scotland/tayside_and_central/5251968.stm bbc article] also known as GSTP1Val105, or GSTP1 Ile105Val This [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16882827&query_hl=1&itool=pubmed_docsum research paper] shows that 13- to 21-year-olds exposed to tobacco smoke at home, with this mutation had more severe asthma than those without the mutation. Several papers published findings associating GSTP1 Ile105Val genotypes with bronchial, childhood, or atopic asthma. Note that some studies, however, have not observed any association between this SNP and asthma in certain populations , or even more paradoxically, have observed that rs1695(G;G)...
35.0	rs12953717 (C;C)	1x normal risk for colorectal cancer

			rs12953717 is one of 3 SNPs in the SMAD7 gene associated with risk for colorectal cancer, based on a large study (7,400+ cases) conducted in the UK. The odds ratios show an increased risk for the minor rs12953717(T) allele; the OR for (T;T) homozygotes is 1.37 (CI: 1.25-1.5), and for (C;T) heterozygotes 1.11 (CI: 1.03-1.2), overall p=9x10^-12.
35.0	rs10494366 (T;T)	Shorter QT interval

			rs10494366, a SNP in the NOS1AP gene encoding the nitric oxide synthase I protein, accounts for some of the variation seen in abnormal heart rhythms, in particular, the QT interval. Based on studies totaling ~4,000 individuals of Caucasian ancestry, homozygotes for one allele have shorter QT intervals, while homozygotes for the other allele have a longer QT interval. A follow-up study determined that one rs10494366(G) allele was associated with a 3.8-ms (CI: 3.0 - 4.6ms, p=7.8x10(-20)) increase in QT interval duration, and two (G) alleles had twice that increase. No increase in risk for sudden death due to a cardiac problem was associated with this SNP, though. rs10494366 minor homozygotes had a 9.3 msec longer QT interval compared to major homozygotes (p=5.7x10(-5)); rs10918594 minor h...
35.0	rs3731239 (T;T)	normal risk

			rs3731239 shows a slight protective association against breast cancer in a British study involving ~2300 patients. The odds ratio for the (C;C) vs (T;T) homozygotes is 0.90 (CI: 0.79-1.03, p=0.013).
35.0	rs10790212 (C;T)

			Category:is a snp associated with schizophrenia rs10790212-rs4938445-rs497768
35.0	rs6587852 (A;C)

			rs6587852 is one of 6 SNPs found upstream of an (uncharacterized) gene known as FLJ10986 that have been found to be overrepresented in 1,152 patients with sporadic amyotrophic lateral sclerosis (ALS).
35.6	rs6458307 (C;T)	0.8x risk

			rs6458307 has been reported in a large study to be associated with bipolar disorder. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated with heterozygotes is 0.84 (CI 0.75-0.96), and for homozygotes, 1.39 (CI 1.13-1.69).
35.6	rs980989 (G;T)

			13 single-nucleotide polymorphisms (SNPs) in 723 members of 179 Finnish Bipolar disorder families. *rs980989 psychomotor processing speed
35.6	rs2300478 (G;T)	1.7x risk for restless legs

			rs2300478, a SNP located in the MEIS1 gene, has been linked to restless legs syndrome, a common sleep disorder, with an overall odds ratio of 1.78 (CI: 1.52-2.09) for the (G) risk allele. The association from this region that gives the highest association to restless legs syndrome, however, is a haplotype consisting of the rs6710341(A) and rs12469063(G) alleles. This haplotype gives rise to an odds ratio of 2.75 (CI: 2.23-3.41).
36.7	rs358806 (A;C)	0.9x risk

			rs358806 has been reported in a large study to be associated with type-2 diabetes. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 0.86 (CI 0.75-0.97), and for homozygotes, 1.78 (CI 1.34-2.36).
36.7	rs4988300 (G;G)

			linked to obesity
36.7	rs4778241 (C;C)	blue eye color if part of blue eye color haplotype

			rs4778241 is part of a haplotype spanning 166kB on chromosome 15, defined by 13 SNPs listed below, found in 97% of all Caucasians with blue eyes. In this haplotype, variations in rs1129038 and rs12913832 are relatively common in Caucasians though rare among other ethnic groups. The 'h-1' haplotype found in homozygous state in 97% of individuals with blue eye color is composed as follows : rs4778241(C) rs1129038(A) rs12593929(A) rs12913832(G) rs7183877(C) rs3935591(G) rs7170852(A) rs2238289(T) rs3940272(C) rs8028689(T) rs2240203(A) rs11631797(G) rs916977(G)
36.7	rs6971091 (A;G)	>2x increased risk for familial obesity

			rs6971091 is a SNP on chromosome 7 that has been linked to obesity. In a study of 400+ patients, rs6971091(A) allele carriers had an odds ratio of at least 2 for obesity defined by both body mass index (BMI) and leptin levels.
36.7	rs7652331 (C;T)	normal risk

			rs7652331 is one of seven SNPs found in a combined study of over 1,000 patients to be associated with increased risk for prostate cancer. The risk allele for this SNP is (T); and while the odds ratio was not specifically reported, the probability of false significance (not permuted though) was given as p=4.4 x 10e-5, using a dominant model of risk.
36.7	rs20541 (C;T)

			rs20541 influences the effect of maternal smoking during pregnancy and persistent childhood asthma
36.7	rs989638 (A;A)

			This SNP is part of a specific haplotype, rs989638-rs1034428-rs2227098 G-T-G (as oriented with respect to dbSNP) with an overall ~2x higher risk in females for schizophrenia (p=0.0008).
36.7	rs10516487 (C;T)

			rs17266594 rs10516487 rs3733197 gene associated with systemic lupus erythematosus.
36.7	rs2437896 (C;T)

			This SNP was identified as a 'core' SNP helping to define one (of nine total) runs of homozygosity (ROH) potentially associated with increased risk for schizophrenia. Each region consists of at least 100 consecutive SNPs, generally spanning 500KB or more, for which both chromosomes in an individual were homozygous. The overall odds ratio for schizophrenia associated with inheriting 1, 2, or 3 of these 9 ROHs was calculated to be 3.3, 5.4, or 24, respectively, with 95% confidence intervals of (1.9-5.7), (3.7-16.1), and (6.9-83.9), respectively. This particular SNP, rs2437896, was deemed to be the core SNP of a region on chromosome 2 with 115 SNPs spanning 774KB from 2:175671012 to 2:176445047 (build 35). Potentially independent of the ROH, the risk allele for this SNP in the orientation as ...
36.7	rs2637777 (T;T)

			associated with bipolar disorder
36.7	rs6700125 (C;T)	1.2x increased risk for ALS

			rs6700125 is one of 6 SNPs found upstream of an (uncharacterized) gene known as FLJ10986 that have been found to be overrepresented in patients with sporadic amyotrophic lateral sclerosis (ALS). A genome-wide association study of 1,152 ALS patients determined an allelic odds ratio of 1.38 for the rs6700125(T) allele (CI: 1.16-1.65, p=0.00032). The genotypic odds ratio presented were 1.76 (CI: 1.22-2.55) and 1.2 (CI: 0.83-1.73) for homozygotes and heterozygotes, respectively. * Note: this SNP is in strong linkage disequilibrium with rs6690993 (r²>0.8)
36.7	rs11276 (G;G)

			[omim:DOMBROCK BLOOD GROUP]
36.7	rs699 (T;T)	normal risk

			rs699 is a SNP in the angiotensin AGT gene that encodes a functional change. In most published literature, the name for this SNP is M235T, or perhaps Met235Thr, however its amino acid 268 (not 235) that varies based on the numbering in todays databases. rs699 is also occasionally known as C4072T. In any case, the rs699(C) allele encodes the threonine variant, which is associated with higher plasma angiotensin levels, and ultimately higher blood pressure leading to increased risk for hypertension associated disorders. This association was first reported in 1992 , and many studies, though not all, have replicated these findings. rs699 is also (generally) reported to be in tight linkage with rs5051, a neighboring SNP in the promoter of the AGT gene. rs699(C) has also been implicated as a risk...
36.7	rs1136287 (C;T)

			Associated with increased risk for wet age-related macular degeneration in a study of Taiwanese Chinese patients.
36.7	rs1042602 (C;C)

			[omim:TYROSINASE POLYMORPHISM]
36.7	rs1948 (C;T)

			The (C;C) genotype (as published) of rs1948 was calculated to represent a hazard ratio of 1.29 (CI: 1.01-1.63) for initiation of tobacco and alcohol use at an earlier age than average. A linked SNP also in the A5A3B4 gene, rs8023462, showed similiar association.
36.7	rs979752 (C;C)

			Associated with type-2 diabetes in a Mexican-American population.
36.7	rs3733890 (A;G)

			Variant BHMT allele may increase risk for neural tube defects, apparently only in folate rich environments, and possibly in conjunction with rs1801133
36.7	rs3791878 (A;C)

			implicated in schizophrenia
36.7	rs10086908 (T;T)	1.7x increased risk for prostate cancer

			rs10086908 is a SNP in the 8q24 chromosomal region, which has been linked in several studies to prostate cancer. In a study of 1,563 patients of European ancestry, rs10086908 was designated as the representative of a prostate cancer risk region termed 'locus 3', with an odds ratio of 1.70 (CI: 1.39-2.07) for carriers of a risk genotype. Two other regions of chromosome 8q24 were also studied.
37.3	rs1545985 (A;G)	somewhat higher risk for prostate cancer

			rs1545985 is one of seven SNPs found in a combined study of over 1,000 patients to be associated with increased risk for prostate cancer. The risk allele for this SNP is (G); and while the odds ratio was not specifically reported, the probability of false significance (not permuted though) was given as p=6.6 x 10e-6, using an additive model of risk.
37.3	rs754618 (A;G)

			affects HIV-1/AIDS
37.9	rs3923809 (A;G)	1.9x risk for restless legs

			This SNP, located in an intron of the BTBD9 gene, has a variant that is seen somewhat more frequently in individuals with restless legs syndrome. The risk allele is rs3923809(A); carriers of two such alleles, i.e. those with rs3923809(A;A) genotypes, are estimated to be 1.9 fold more likely to have restless legs syndrome than rs3923809(G;G) individuals. The authors of this study suggest that perhaps half of the cases of restless legs syndrome may involve the rs3923809 risk genotypes. Consistent with this finding, another report about rs3923809 links the (G) minor allele to a lower frequency of restless legs syndrome with an overall odds ratio of 0.57 (CI: 0.48-0.68). Note that 70-80% of all individuals in European populations carry one or two copies of the (A) major allele, yet restless ...
38.3	rs1494555 (C;T)

			[omim:SEVERE COMBINED IMMUNODEFICIENCY, AUTOSOMAL RECESSIVE, T CELL-NEGATIVE, B CELL-POSITIVE, NK CELL-POSITIVE]
38.3	rs36686 (A;G)

			rs36686, a SNP in the B3GNT3 gene also known as H328R, is associated with reduced risk for developing Non-Hodgkin Lymphoma based on a study of 458 patients. The odds ratio is 0.74 (CI: 0.59-0.93, p<0.01).
38.3	rs1329428 (A;G)	?

			linked to blindness in age related macular degeneration rs3753394, rs800292, rs1061147, rs1061170, rs380390, and rs1329428 Significant associations were detected for AMD with rs3753394 rs800292 rs1329428 A haplotype of rs1061170 rs3753394 rs800292 rs1329428 (TGTC) was found to confer a significantly increased likelihood of exudative AMD CFH variations appear to contribute to ARMD in Caucasians, but not in Japanese
38.3	rs4149601 (G;G)

			rs4149601 has been associated with hypertension. This SNP by itself was associated with diastolic blood pressure (DBP) (p=0.03) and DBP progression over time (p=0.04); in genotypic combination with intronic NEDD4L SNP rs2288774 it was associated with systolic blood pressure (SBP) (p=0.01), DBP (p=0.04), and progression of both SBP (p=0.03) and DBP (p=0.05) over time.
38.3	rs2076756 (A;A)	normal

			rs2076756 is a SNP of the NOD2 gene found in a genome-wide association study to be associated with Crohn's disease. In several European populations, the minor NOD2 allele, rs2076756(G), is associated with increased risk for Crohn's disease. The odds ratio (pooled over several populations) is 1.71 (CI: 1.42-2.05, p=6x10^-8).
38.3	rs7923837 (A;G)	1.6x risk for T2D

			rs7923837 is a SNP of the HHEX homeobox gene. In several studies, it has been associated with risk for type-2 diabetes (T2D). In a study of 500 unrelated Caucasian T2D patients, the rs7923837(G) allele was overrepresented; the odds ratio was 1.57 (CI: 1.08-2.27, p=0.017). In this population, the population attributable risk for this allele was estimated to be 33%. In a study of ~400 Japanese T2D patients, rs7923837(G) was also associated with type-2 diabetes (odds ratio 1.66, CI: 1.28-2.15, p=0.00014). Heterozygous and homozygous carriers of the risk allele had odds ratios of 1.57 (95% CI 1.15-2.16, p=0.0050) and 3.16 (95% CI 1.40-7.16, p=0.0038) relative to non-carriers.
38.3	rs988213 (A;G)

			This SNP was associated with amyotrophic lateral sclerosis (ALS) based on a study of 1,152 patients.
38.3	rs1051730 (C;C)	normal

			rs1051730, also known as D398N, is a SNP in the nicotinic acetylcholine receptor alpha 3 subunit CHRNA3 gene. In two recent (2008) studies, together comprising over 6,000 lung cancer patients of European ancestry, the rs1051730(T) allele was very significiantly associated with increased risk. Having one copy (i.e. being a rs1051730(C;T) genotype) increased risk for lung cancer about 1.3x, and having two copies (rs1051730(T;T) individuals) represented 1.8x increased risk. Up to 14% of lung cancer incidence may be attributable to this allele.[PMID 18385738, PMID 18385676] An independent study published at the same time concluded that (T) allele carriers for SNP rs1051730 are not at higher risk of becoming smokers compared to (C) carriers. However, if they do smoke, (T) carriers are quite lik...
38.3	rs807701 (T;T)	common

			Rs807701, a SNP in the DCDC2 gene, is in a region that crops up in several independent studies as likely to associated with dyslexia. The risk allele in the Caucasian populations studied is (A). One study reports that the odds ratio for rs807701 genotypes increases if calculated from subsets of more severely dyslexic individuals as compared to more heterogenous, larger groups of dyslexic individuals. The genotype relative risk (GRR) for rs807701(C;C) increased from 1.88 (95% CI 0.893.97; P=.058) for the larger group up to 5.04 (95% CI 1.3518.88; P=.002) for the most severely affected group. Combined with another SNP marker in the DCDC2 gene, rs793862, the (haplotype) GRR also increased for the homozygous haplotype rs793862(A)-rs807701(C), from 4.11 (95% CI 2.776.08; P<.0001) for the la...
38.3	rs2858331 (C;T)

			Source [http://www.nature.com/ng/journal/v38/n10/fig_tab/ng1885_T1.html nature] Celiac diseased rs4988889(T) + rs2858331(C)
38.3	rs39317 (G;G)

			SNP rs39317 has been associated with both cholesterol levels and low-density lipoprotein levels in the Framingham Heart Study datasets, and is thus associated with heart disease. [http://gmed.bu.edu/about/analysis.html source]
38.3	rs1494558 (A;G)

			[omim:SEVERE COMBINED IMMUNODEFICIENCY, AUTOSOMAL RECESSIVE, T CELL-NEGATIVE, B CELL-POSITIVE, NK CELL-POSITIVE]
38.3	rs3738919 (C;C)	1.9x risk

			rs3738919, a SNP located in the ITGAV gene, was identified in a European study to be associated with rheumatoid arthritis (RA). The risk allele for rs3738919 is the more common allele, (C). For the three European Caucasian populations studied (372 RA patients + 330 controls), and combining the (C;C) and (A;C) genotypes in comparison to the (A;A) genotype, the odds ratio for RA = 1.94 (CI: 1.32.9, p = 0.002). There was no significant difference in RA risk between those carrying one or two (C) alleles. An editorial about this finding has been published.
38.3	rs780094 (G;G)	average

			rs780094, a SNP in the GCKR gene encoding the glucokinase regulatory protein, appears to be associated with several metabolic consequences, based on a study of ~15,000 Danes. The minor allele, rs780094(A), is the risk allele, and it is associated with the following traits : * higher levels of fasting serum triacylglycerol * impaired fasting and OGTT-related insulin release * dyslipidemia * somewhat reduced risk of type-2 diabetes There may also be an additive effect between this SNP and a SNP known as 'GCK -30A', rs1799884, at least on fasting serum insulin levels.
38.6	rs4504469 (C;C)	common

			Rs4504469, a nonsynonymous SNP in exon 4 of the KIAA0319 gene, is in a region that crops up in several independent studies as likely to associated with dyslexia. The risk allele in the Caucasian populations studied is (T). The odds ratio in a study of case:control study of ~400 Caucasians associated with rs4504469(T) is 1.51 (CI: 1.171.95, p = 0.002).
38.9	rs11200014 (A;G)	1.20x risk for breast cancer

			This SNP is basically a proxy for SNP rs1219648, which represents the SNP in the FGFR2 gene with the strongest association with breast cancer.
39.0	rs4988235 (C;T)	can digest milk

			Also known as 'C/T(-13910)', and located in the MCM6 gene but with influence on the lactase LCT gene, rs4988235 is one of two SNPs that is associated with the primary haplotype associated with hypolactasia, more commonly known as lactose intolerance in European Caucasian populations. , In these populations, the rs4988235(T) allele is both the more common allele and the one associated with lactase persistence; individuals who are rs4988235(C;C) are likely to be lactose intolerant. In populations of sub-Saharan Africans, though, the rs4988235(T) allele is so rare that it's unlikely to be predictive of lactase persistence, and other SNPs are predictive instead. [PMID 15106124, PMID 17159977] * See also [http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=601806&a=601806_AllelicVariant0001 OMIM...
39.7	rs1501299 (A;C)

			breast cancer. 733 hospital-based breast cancer cases and 839 controls rs2241766(T;G): OR, 0.61; 95% CI, 0.46-0.80 rs1501299(G;G): odd ratios (OR), 1.80; 95% confidence interval (95% CI), 1.14-2.85; *rs7539542 associated with breast cancer risk (OR, 0.51; 95% CI, 0.28-0.92) when compared with high signalers, intermediate signalers had a 4.16-fold increase in breast cancer risk (95% CI, 0.49-35.19), and low signalers had a 6.56-fold increase in breast cancer risk (95% CI, 0.78-54.89; P(trend) = 0.001).
39.7	rs2420946 (C;T)	1.20x risk for breast cancer

			This SNP is basically a proxy for SNP rs1219648, which represents the SNP in the FGFR2 gene with the strongest association with breast cancer.
40.0	rs1143627 (T;T)

			associated with ankylosing spondylitis risk of Helicobacter pylori infection. Children carrying IL1A-889T had a lower risk of H. pylori positivity, compared to those carrying -889C, with each T allele associated with 43% risk reduction (OR = 0.57, 95% CI = 0.33-0.99, p-trend = .05) upregulation of pro-inflammatory cytokines may protect against persistent H. pylori colonization.
40.0	rs7008482 (G;T)

			Two genetic markers in the 8q24 region of chromosome 8 rs7008482 and rs16901979 have been linked to an increased risk of prostate cancer in African Americans. [http://www.genome.org/cgi/content/abstract/gr.6782707v1 abstract]
40.0	rs6165 (A;G)

			[omim:OVARIAN RESPONSE TO FSH STIMULATION]
40.0	rs662 (A;A)

			Variations in this SNP, corresponding to amino acid 192 of the PON1 protein, are correlated with Heart disease. The normal form, rs662(A), encodes a glutamine, while the variant, rs662(G)), encodes an arginine. . While some populations show an association between this SNP and Heart disease, not all do. Perhaps the most striking finding was reported in Japanese patients with non-insulin dependent diabetes mellitus (NIDDM). NIDDM patients with either one or two rs662(G) alleles had a 9 fold higher risk of coronary heart disease compared with rs662(A,A) NIDDM patients. [http://www.theheart.org/article/848219.do table] of odds for cardiovascular disease outcomes [omim:CORONARY ARTERY DISEASE, SUSCEPTIBILITY TO]
40.0	rs1219648 (A;G)	1.20x risk for breast cancer
			This is the genotype of User:Watson
			Based on a study of ~2500 female patients of European ancestry with sporadic postmenopausal breast cancer, this SNP in the FGFR2 showed the greatest risk. The risk allele is rs1219648(G), with a pooled odds ratio of 1.64 (CI:1.42-1.90) for rs1219648(G;G) homozygotes, and an odds ratio of 1.20 (CI: 1.07-1.42) for rs1219648(A;G) heterozygotes, compared with rs1219648(A;A) homozygotes. rs1219648 represents the SNP in the FGFR2 gene with the strongest association with breast cancer. However, nearby SNPs are almost as predictive. In particular, the following SNP alleles all have linkage values of 0.96 or greater with the rs1219648(G) allele in European populations: rs2981579(A) rs2420946(T) *rs11200014(A) An experimental rationale is presented indicating that this SNP is part of a haplotype t...
40.0	rs2235015 (G;T)	7x more likely to respond to certain antidepressants

			rs2235015 is a SNP in the ABCB1 gene (also known as the MDR1 gene), which encodes a protein that transports certain molecules across the blood-brain barrier. SNPs in ABCB1 may thus influence the intracerebral concentrations of certain drugs and thus their efficacy or potential for adverse side effects. rs2032583 is near 9 SNPs found within a tight linkage block (r² >= 0.8 ) such that the minor allele at any one of them predicts (with ~80%+ accuracy) that the other SNPs will also be the minor allele. The list of the 9 SNPs is shown below. rs2235015 has an r² value of >0.5 with this group. When treated for depression with substrates of the protein encoded by ABCB1, carriers of one or two minor alleles at these ABCB1 SNPs have been reported to respond better than non-car...
40.0	rs30187 (C;T)	1.4x higher risk for spondylitis

			rs30187 is one of several SNPs in the ARTS1 gene that has been shown in a large (over 1,000 Caucasian patients) study to be associated with ankylosing spondylitis. The odds ratio is 1.40 (p=3.4x10e-10).[PMID 17952073, PMID 18037607]
40.0	rs6996321 (A;G)

			rs6996321 significantly related to spine bone mineral density (p=0.002) and rs10914367 associated with hip BMD (p=0.028). Non-vertebral fracture risk was significantly increased in carriers of 'A' allele of rs9900972 (OR=2.06, p=0.0187)
40.0	rs9551963 (A;C)

			rs9551963, also known as SG13S32, is an ALOX5AP gene SNP that has been defined as part of a haplotype potentially associated with risk for myocardial infarction or ischemic stroke. Details of this haplotype and several related studies are on the ALOX5AP page.
40.0	rs6166 (A;G)	normal risk

			rs6166, also known as Asn680Ser, is a SNP in the follicle stimulating hormone receptor FSHR gene. rs6166(G) is the risk allele encoding the Ser amino acid, at least based on one study in which less fecund women were found to be disproportionately Ser/Ser homozygotes (i.e. rs6166(G;G) homozygotes; p=0.0035). [omim:OVARIAN RESPONSE TO FSH STIMULATION]
40.0	rs3740066 (G;G)	average

			rs3740066, a SNP in the ABCC2 gene, is reported to be associated with a higher risk of developing intrahepatic cholestasis of pregnancy (ICP) based on a study of ~70 Argentinian patients. ICP is associated with increased fetal risks such as premature birth or intrauterine death. The risk allele is rs3740066(A), and the odds ratio for homozygous rs3740066(A;A) mothers is 4.44 (CI: 1.83 - 10.78), and for heterozygous mothers 1.65 (CI: 0.76 - 3.64), compared to rs3740066(G;G) mothers.
40.4	rs1495965 (A;G)	1.2x higher risk for spondylitis

			rs1495965 is one of several SNPs in the IL23R gene that has been shown in a large (over 1,000 Caucasian patients) study to be associated with ankylosing spondylitis. The odds ratio is 1.2 (p=6.6x10e-6).[PMID 17952073, PMID 18037607]
40.7	rs6598 (A;G)

			Patients with the minor allele A of rs6598 had an increased prevalence of IA-2 autoantibody levels compared to patients without the minor allele (OR=2.2; Bonferroni-corrected P=0.003). is associated with islet autoimmunity in type I diabetes other autoimmune disease.
40.7	rs2981579 (C;T)	1.20x risk for breast cancer

			This SNP is basically a proxy for SNP rs1219648, which represents the SNP in the FGFR2 gene with the strongest association with breast cancer. {Note: the alleles shown for this SNP in SNPedia are in orientation to the dbSNP entry, not as published.]
41.4	rs1411771 (C;T)

			13 single-nucleotide polymorphisms (SNPs) in 723 members of 179 Finnish Bipolar disorder families. rs751229(T) and rs3738401(A) was over-transmitted to males with psychotic disorder. under-transmitted rs821616(T) and rs1411771(T) *The risk haplotype for psychotic disorder also associated to perseverations (P = 0.035; for rs751229 alone P = 0.0012), and a protective haplotype G-T-G with rs1655285 in addition to auditory attention (P = 0.0059).
41.7	rs11887120 (C;C)

			829 Caucasian cases with primary epithelial ovarian cancer and 941 frequency-matched unaffected controls Three SNPs in DNMT3A were associated with risk among multivitamin supplement users: 3' untranslated region (UTR) C>G (rs13420827: OR, 0.8; 95% CI, 0.6-1.0; P interaction = 0.006; FPRP = 0.54) intron 6 G>A (rs11887120: OR, 0.8; 95% CI, 0.7-1.0; P interaction = 0.007; FPRP = 0.57) *intron 22 A>T (rs11695471: OR, 1.2; 95% CI, 1.0-1.5; P interaction = 0.01; FPRP = 0.66)
41.7	rs287354 (C;C)

			SNP rs287354 has been associated with both cholesterol levels and low-density lipoprotein levels in the Framingham Heart Study datasets, and is thus associated with heart disease. [http://gmed.bu.edu/about/analysis.html source]
41.7	rs4344 (A;G)	slower responder

			This SNP in the ACE gene, also known as G12269A, is reported to influence how quickly African Americans respond to the anti-hypertensive drug ramipril. rs4344(A;A) and rs4344(G;G) homozygotes are able to reach lower blood pressure levels upon treatment with ramipril sooner than rs4344(A;G) heterozygotes. The odds ratio reported for this study, comparing both homozygotes to heterozygotes, is 1.86 (CI: 1.32-3.23). Note that this SNP is in almost complete linkage disequilibrium with the insertion/deletion ACE gene SNP.
41.7	rs1049623 (A;G)

			schizophrenia rs1049623 associated with schizophrenia (odds ratio=1.44, 95% confidence interval: 1.15-1.79, adjusted P=0.0016). schizophrenia the SNPs (rs1049623, rs2267641 and rs2239518) haplotype remaining significant even after adjustment for multiple testing (adjusted P=0.0136).
41.7	rs603965 (A;G)	?

			rs603965 is a SNP in the cyclin D1 CCND1 gene. It is also known as Pro241Pro. The associated genotypes are characterized in terms of their enzymatic activity as High for (A;A), Medium (A;G), and Low (G;G). In a study of 2 populations of breast cancer patients (2,000+ patients), increased risk was associated with rs603965(A;A) genotypes in both the Ontario [odds ratio 2.22, CI: 1.49-3.28] and Finland [OR 1.73, CI: 1.08-2.78] populations.
41.7	rs1571801 (A;C)	1.36x risk for prostate cancer

			In a study of ~1000 Caucasian patients with prostate cancer, rs1571801 was the SNP most associated with not only prostate cancer, but having an aggressive form of it. The odds ratio for aggressive prostate cancer associated with the risk allele, rs1571801(A), was 1.36 (CI: 1.13 - 1.65, p = 0.001). The odds ratio associated with (nonaggressive) prostate cancer was also higher than average for this SNP; for the same (A) risk allele, it was 1.27 (CI: 1.10 - 1.48, p = 0.0017). Although the association was found in a study of Caucasian patients, it was also reported to be statistically significant in a population of 210 African-Americans with prostate cancer. According to [http://www.oncology-information.com/CancerLineHCP/6096_31566_2__.aspx], 'The odds ratio for aggressive prostate cancer ra...
41.7	rs1061147 (A;C)
			This is the genotype of User:Watson
			may influence age related macular degeneration when part of the haplotype of rs1061170 rs3753394 rs800292 rs1329428 (TGTC), but does not appear to do so alone.
41.7	rs13146272 (A;C)

			[http://jama.ama-assn.org/cgi/content/short/299/11/1306 jama] deep vein thrombosis per risk allele odds ratio rs13146272 in CYP4V2 (risk allele frequency, 0.64) OR 1.24 (95% CI, 1.11-1.37) for rs13146272 rs2227589 in SERPINC1 (risk allele frequency, 0.10) OR 1.29 (95% CI, 1.10-1.49) for rs2227589 *rs1613662 in GP6 (risk allele frequency, 0.84) OR 1.15 (95% CI, 1.01-1.30) for rs1613662
41.7	rs2989727 (C;T)

			the A allele rs2989727 was significantly increased in RA patients (67%) compared with controls (60%) (P = 0.002). Also, the frequency of the G allele of rs1071583 was increased in RA patients (68%) compared with controls (61%) (P = 0.003).
41.7	rs741301 (A;A)

			Associated with diabetic nephropathy and type-2 diabetes in a Japanese population.
41.7	rs11209032 (A;G)	1.3x higher risk for spondylitis

			rs11209032 is one of several SNPs in the IL23R gene that has been shown in a large (over 1,000 Caucasian patients) study to be associated with ankylosing spondylitis. The odds ratio is 1.3 (p=7.5x10e-9).[PMID 17952073, PMID 18037607]
42.4	rs2167270 (A;G)	normal

			rs2167270 is a SNP in the leptin LEP gene. In a study of ~1,500 colon cancer patients, the rs2167270(A;A) genotype was underrepresented, leading to an odds ratio of 0.79 (CI: 0.64-0.98).
42.4	rs12970134 (G;G)	normal

			A study of 14,000 Indian Asian or Caucasian adults indicates that rs12970134(A) alleles are associated with larger waist circumference. The average increase in waist circumference is 0.9cm BMI units per risk allele.[PMID 18454146; see also [http://spittoon.23andme.com/2008/05/04/snpwatch-mc4r-gene-associated-with-body-mass/
42.4	rs6604026 (C;T)	1.15x risk

			rs6604026 has been reported in a large study to be associated with multiple sclerosis. The risk allele (oriented to the dbSNP entry) is (C); the odds ratio associated with this allele is 1.15 (CI 1.08-1.22).
42.6	rs9340799 (A;G)

			rs9340799 is a SNP in the estrogen alpha receptor ESR1 gene, and it is also known as the -351A>G variant. Among women rs8179176 rs9340799 rs1256065 and rs1256030 were associated with likelihood of developing cognitive impairment. In men, one of the rs728524 rs1255998 rs1256030 were associated with cognitive impairment. A study of 6,200+ Dutch individuals did not replicate previously reported associations between this SNP (rs9340799) and risk of ischemic stroke
43.1	rs3737787 (C;C)

			contributes to high serum lipid levels in Dutch familial combined hyperlipidemia families and U.S. whites with coronary artery disease [omim:HYPERLIPIDEMIA, FAMILIAL COMBINED, SUSCEPTIBILITY TO]
43.3	rs2165241 (C;C)	normal

			This SNP, located in an intron of the LOXL1 gene, was initially reported to be associated with exfoliation glaucoma. However, it was shown in the same study to no longer be significant once two other SNPs, which cause actual changes in the LOXL1 protein, were identified. More specifically, the risk allele rs2165241(T) was found to be associated with glaucoma only because it effectively predicted (with 90% probability) the actual high-risk haplotype consisting of rs1048661(G) and rs3825942(C), as oriented with respect to their entries in dbSNP. rs2165241 was significantly associated with XFG and XFS (p=4.13x10e-9 for an additive model, heterozygote odds ratio = 4.42 (CI: 2.3-8.5), homozygote odds ratio = 34.19 (CI: 4.48-261), with the rs2165241 (T) allele being the risk allele, found in 8...
43.3	rs16942 (A;A)

			This SNP, a variant in the BRCA1 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (G).
43.3	rs1799966 (A;A)

			This SNP, a variant in the BRCA1 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (G).
43.3	rs3755351 (C;C)	>1.3x risk for hypertension

			rs3755351, a SNP in the ADD2 gene, was associated with risk for hypertension in a study involving 1,500+ Japanese patients. The odds ratio associated with the risk allele, rs3755351(C), which is also the most common allele, is 1.30 (CI: 1.15 - 1.46, p = 0.00002). Note that a neighboring ADD2 SNP in close (r2 of 0.806) proximity, rs17006246, was associated with hypertension in a diabetes study ; however, in this case, it was in 'the opposite direction of effect'. This discrepancy has not been resolved.
43.3	rs3792267 (A;G)

			summary, indicating a small effect of this SNP, seen only in meta-analyses rs3792267 associated with noninsulin-dependent diabetes mellitus, polycystic ovary syndrome, type 2 diabetes, gestational diabetes and obesity
43.3	rs4415084 (C;T)

			[http://www.nature.com/ng/journal/vaop/ncurrent/abs/ng.131.html nature] 6,145 cases and 33,016 controls rs4415084 and rs10941679 confer risk for estrogen receptor breast cancer (ER)-positive tumors (OR = 1.27, P = 2.5E-12 for rs10941679).
43.3	rs806380 (A;G)

			This snp, located in intron 2 of the central cannabinoid receptor CNR1 gene, has been linked to cannabis dependence. The (G) allele is reported to have a protective effect, and is a defining part of a haplotype that is associated with lower odds of developing cannabis dependence. The (A) allele is more common in all populations studied.
43.3	rs439401 (C;C)

			This appears to be the snp on the Illumina Human 550 which is closest to rs4420638
43.3	rs1799990 (A;G)

			[omim:PRION DISEASE, SUSCEPTIBILITY TO]
43.3	rs952635 (A;A)

			rs2863389, rs7935082 and rs952635 implicated in type-2 diabetes by
43.3	rs643627 (A;G)

			Three (rs643627-rs594242-rs6311: A-C-T), two (rs594242-rs6311: C-T) and a single functional (rs6311: T) marker were protective against suicidal behavior. The complementary makers (rs594242-rs6311: G-C and rs6311: C) were associated with increased risk for non-violent and impulsive suicidal behavior. Furthermore, CC-homozygotes for the functional SNP rs6311 reported more anger- and aggression-related behavior.
43.3	rs4763655 (G;G)	common

			rs4763655 has been reported in a large study to be associated with multiple sclerosis. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with this allele is 1.10 (CI 1.04-1.17).
43.3	rs3847953 (G;G)

			rs3847953 and rs933399 associated with bipolar disorder
43.3	rs839523 (A;G)

			linked to schizophrenia with rs7598440, rs839523, and rs707284
43.3	rs2293275 (A;G)

			SNP in the luteinizing hormone/chorionic gonadotropin receptor (LHCGR) gene, correlated to spermatogenetic damage and thus a risk factor for male infertility.
43.3	rs754499 (G;T)

			Suspected of reproducibility problems based on [http://www.kk.org/quantifiedself/2008/05/testing-genetic-test-chips.php end user analysis] rs11149566 rs4458717 rs4660646 rs754499
43.3	rs560887 (A;G)

			rs560887, p = 4 x 10(-7)) 654 normoglycemic subjects, replicated in 9,353 subjects fasting plasma glucose (FPG) (beta = -0.06 mmol/l per A-allele, combined p = 4 x 10(-23)) and with pancreatic beta-cell function (Homa-B model, combined p = 3 x 10(-13)) in three populations; however it was not associated with type 2 diabetes risk.
44.1	rs4276227 (C;C)	1.5x risk

			rs4276227 has been reported in a large study to be associated with bipolar disorder. The risk allele (oriented to the dbSNP entry) is (C); the odds ratio associated with heterozygotes is 1.2 (CI 0.99-1.46), and for homozygotes, 1.49 (CI 1.23-1.81).
44.6	rs1135062 (A;G)

			[omim:AUBERGER BLOOD GROUP POLYMORPHISM Au(a)/Au(b)]
45.0	rs8050894 (C;C)	warfarin sensitivity (~2.5 mg/day)

			rs8050894, is located on chromosome 16 in the gene VKORC1. VKORC1 is the primary target of the drug warfarin (Coumadin), a commonly used oral anticoagulant. rs8050894 is one of several polymorphisms found in VKORC1 that is associated with specific warfarin doses (). Other polymorphisms in VKORC1 (rs7196161, rs9923231, rs9934438, rs2359612) are equally predictive of warfarin dose requirement in both European and Asian-descent individuals. Other polymorphisms found in the gene cytochrome P450 2C9 (CYP2C9) influence the metabolism of warfarin and have a smaller effect on warfarin dose. These polymorphisms are rs1799853 (CYP2C92) and rs1057910 (CYP2C93).
45.0	rs1804495 (G;G)

			[omim:THYROXINE-BINDING GLOBULIN, VARIANT P]
45.0	rs10239794 (C;T)	1.3x risk for ALS

			rs10239794, a SNP in the region of the DPP6 gene on chromosome 7, has been associated with the sporadic form of ALS (Lou Gehrig's disease) in a study of 1000+ European patients. The odds ratio for the risk allele rs10239794(C) is 1.30 (CI: 1.18 - 1.43). A 'CC' haplotype for this SNP and that of it's neighbor rs10260404 is also highly (statistically; p=10e-9) associated with ALS.
45.0	rs1801131 (A;C)

			[omim:MTHFR THERMOLABILE POLYMORPHISM]
45.0	rs9951307 (A;G)	0.10 decreased risk for brain edema after a stroke

			rs9951307is a SNP in the aquaporin-4 (AQP4) gene; the corresponding protein is the main water channel in the brain and is implicated in the development of brain edema after an ischemic stroke. A study of 41 patients with middle cerebral artery occlusion with and without severe brain edema found that rs9951307 was associated with severe brain edema (dominant model, p=0.01; OR, 0.10, CI: 0.02 to 0.49 for the protective (G) allele).
45.0	rs3784709 (C;C)	common

			rs3784709, a SNP located in a region of chromosome 15q, has been linked to a lower frequency of restless legs syndrome, a common sleep disorder, with an overall odds ratio of 0.71 (CI: 0.60-0.83) for the (T) minor allele.
45.0	rs10798269 (A;G)

			One of several SNPs found in a study of ~2,5720 female patients of European ancestry to be associated with systemic lupus erythematosus.
45.0	rs1454626 (A;C)

			associated with carotid artery disease, BMI, and LDL-associated apolipoprotein B
45.0	rs2077119 (G;T)	0.91x decreased risk for T2D

			rs2077119, also known as -469T/G, is a SNP in the alpha-2-HS-glycoprotein AHSG gene. In a study of ~3,800 Danish type-2 diabetes patients, pooled with a previous study, the minor rs2077119(G) allele showed a slight protective effect, with an odds ratio of 0.91 (CI: 0.84-0.99, p=0.007).
45.0	rs1051740 (T;T)

			[omim:LYMPHOPROLIFERATIVE DISORDERS, SUSCEPTIBILITY TO]
45.0	rs7582658 (A;G)

			This SNP was identified as a 'core' SNP helping to define one (of nine total) runs of homozygosity (ROH) potentially associated with increased risk for schizophrenia. Each region consists of at least 100 consecutive SNPs, generally spanning 500KB or more, for which both chromosomes in an individual were homozygous. The overall odds ratio for schizophrenia associated with inheriting 1, 2, or 3 of these 9 ROHs was calculated to be 3.3, 5.4, or 24, respectively, with 95% confidence intervals of (1.9-5.7), (3.7-16.1), and (6.9-83.9), respectively. This particular SNP, rs7582658, was deemed to be the core SNP of a region on chromosome 2 with 274 SNPs spanning 2282KB from 2:188489676 to 2:190772106 (build 35). Potentially independent of the ROH, the risk allele for this SNP in the orientation as...
45.0	rs173686 (C;T)

			The presence of an rs173686(C) allele has been linked to increased risk of a certain type of stroke, Intracranial Aneurysm, in a population of Dutch adults. Note: the dbSNP sequence entry for this SNP represents the noncoding strand, and is thus the reverse complement compared to the SNP as referred to in .
45.8	rs237025 (C;T)	MET/VAL moderate [[diabetes]] susceptibility
			This [http://www.emaxhealth.com/23/6527.html press release] provides a helpful summary of . The paper concludes that in rs237025, the MET form increases the odds of type-1 diabetes. This form produces both MET and VAL. suggests the contribution of rs237025 to both type-1 diabetes\|type 1 and type-2 diabetes\|type 2 diabetes susceptibility.
			suggests the contribution of rs237025 to both type-1 diabetes\|type 1 and type-2 diabetes\|type 2 diabetes susceptibility. It is also known as Met55Val or A163G. This [http://www.emaxhealth.com/23/6527.html press release] provides a helpful summary of . The paper concludes that in the M55V mutation, the MET form increases the odds of type-1 diabetes. This was the first snpedia snp and has one of the largest (aka most difficult) Watson aligments.
45.8	rs12593813 (G;G)	common

			rs12593813, a SNP located in a region of chromosome 15q, has been linked to a lower frequency of restless legs syndrome, a common sleep disorder, with an overall odds ratio of 0.71 (CI: 0.60-0.83) for the (A) minor allele.
45.8	rs2774279 (C;T)

			The minor allele of rs2774279 was less common among individuals with metabolic syndrome than among healthy controls [p = 0.0029; p = 0.0073]. The minor allele of rs2774279 was also associated with lower BMI, lower fasting glucose values and higher HDL-cholesterol concentrations in longitudinal analyses.
45.8	rs11635424 (G;G)	common

			rs11635424, a SNP located in a region of chromosome 15q, has been linked to a lower frequency of restless legs syndrome, a common sleep disorder, with an overall odds ratio of 0.70 (CI: 0.59-0.82) for the (A) minor allele.
46.6	rs9470080 (C;C)

			rs9296158 rs3800373 rs1360780 rs9470080 linked with the severity of child abuse to predict level of adult PTSD symptoms after correcting for multiple testing.
46.7	rs4792311 (A;G)	increased risk

			[omim:PROSTATE CANCER, SUSCEPTIBILITY TO]
46.7	rs4917 (C;C)

			rs4917 is thought to regulate body fat levels and insulin sensitivity. see obesity [http://www.apollolipids.org/cms/templates/article.aspx?articleid=5201&zoneid=1 link1] the MET/MET genotype has been previously linked with reduced plasma lipid levels and lower body fat concentrations. [http://cat.inist.fr/?aModele=afficheN&cpsidt=16815755 link2] Homozygosity for the rs2593813:G-rs4917:Met-rs4918:Ser haplotype conferred an increased risk for leanness (odds ratio=1.90, P=0.027).
46.7	rs1205 (C;T)

			Although somewhat lacking in statistical power, several reports have linked rs1205, a synonymous mutation known as CRP4 in the C-reactive protein CRP to the autoimmune disorder SLE, systemic lupus erythematosus. The risk allele in dbSNP orientation is (T). [PMID 14645206, PMID 15897982] [omim:C-REACTIVE PROTEIN, PENTRAXIN-RELATED; CRP]
46.7	rs654136 (A;G)

			[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1196416] May Underlie Susceptibility to Adolescent-Onset Idiopathic Generalized Epilepsy
46.7	rs6311 (C;T)

			Three (rs643627-rs594242-rs6311: A-C-T), two (rs594242-rs6311: C-T) and a single functional (rs6311: T) marker were protective against suicidal behavior. The complementary makers (rs594242-rs6311: G-C and rs6311: C) were associated with increased risk for non-violent and impulsive suicidal behavior. Furthermore, CC-homozygotes for the functional SNP rs6311 reported more anger- and aggression-related behavior. This SNP has also been reported to be part of a haplotype associated with risk for rheumatoid arthritis. In this report, the risk allele is rs6311(C). [PMID 18006541
46.7	rs13387042 (A;G)

			rs13387042(A;A) on has an estimated 1.44-fold greater risk than noncarriers,
46.7	rs2075685 (G;T)

			18067C>T possibly related to non-Hodgkin lymphoma rs2040639-AG, contribute to oral cancer risk. pseudo-haplotype with AG-CC genotypes in 2.45x risk rs2040639-rs861539 5.03x risk rs2040639-rs861539-rs2075685 *10.10x risk rs2040639-rs861539-rs2075685-rs1799782
46.7	rs4673 (C;C)

			[omim:CYBA POLYMORPHISM 242C-T]
46.7	rs916055 (C;T)

			rs2619112 and rs916055 are associated with high bone mineral density in pre-menopausal women but low BMD in post-menopausal women
46.7	rs6313 (C;T)	higher risk for RA

			rs6313 is part of a 4-SNP haplotype in the serotonin 2A receptor gene HTR2A that has been associated with rheumatoid arthritis in a study of 1800 European patients. The risk allele is rs6313(C). The overall risk for the haplotype CTCC of SNPs rs6311-rs1328674-rs6313-rs6314 is 1.68 (CI: 1.20 - 2.34, p = 0.02). Note: the orientation of rs1328674 in dbSNP is opposite that cited by this publication; therefore, with respect to dbSNP, the haplotype of risk as cited above is CACC rather than CTCC. see also gs108
46.7	rs729302 (A;A)

			Systemic Lupus Erythematosus rs10488631 rs2004640 rs10954213 and rs729302
46.7	rs6438552 (A;A)

			may influence Parkinson's disease
46.7	rs910586 (C;C)

			rs910586, rs2819861, and rs1934328 may influence cleft palate
46.7	rs10492519 (A;G)	somewhat higher risk for prostate cancer

			rs10492519 is one of seven SNPs found in a combined study of over 1,000 patients to be associated with increased risk for prostate cancer. The risk allele for this SNP is (G); and while the odds ratio was not specifically reported, the probability of false significance (not permuted though) was given as p=5.6 x 10e-6, using an additive model of risk.
46.7	rs3194051 (A;G)	1.12x risk

			rs3194051, one of several SNPs in the IL7R gene, has been reported in a large study to be associated with type-1 diabetes. In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for this SNP was recalculated to be 1.12 (CI 1.051.19).
46.7	rs175174 (A;A)

			This snp in the gene ZDHHC8 does not appear to have any link to schizophrenia despite being quite popular in pubmed
46.7	rs7517847 (G;T)

			significant associations with rs1004819, rs7517847, and rs11209026. Having any CARD15 variant was associated with a significant risk for Crohn's disease (P < 0.0001). rs7517847 (P=4.9x10(-9), OR 0.65, 0.56-0.75), is statistically independent of rs11209026.
47.4	rs4565946 (C;T)
			This is the genotype of User:Watson
			rs4570625 and rs4565946 linked to the pathogenesis of early-onset obsessive compulsive disorder
47.5	rs1050565 (A;G)	normal

			Testicular cancer patients may be treated with bleomycin, a cytotoxic drug that is essential component of chemotherapy regimens for this cancer, officially known as disseminated testicular germ-cell cancer (TC). rs1050565 is a SNP in the BLMH gene. This gene encodes a protein that can inactivate bleomycin. Based on a study of 300 TC patients treated with bleomycin, a testicular cancer patient with a rs1050565(G;G) genotype has an odds ratio of 4.97 (CI: 2.17 - 11.39) for TC-related death compared to (A;G) or (A;A) genotypes. The rs1050565(G;G) genotype also shows a higher prevalence of early relapses.
47.9	rs25487 (G;G)	2x higher risk for skin cancer

			rs25487 is a SNP also known as Gln399Arg, located in the DNA repair gene XRCC1. The (A) allele encodes the Gln amino acid. In one study of ~1000 Caucasians, the rs25487(A;A) genotype had significantly reduced risk of both basal cell [BCC; odds ratio 0.7, CI: 0.4-1.0] and squamous cell cancer (SCC; odds ratio 0.6, CI: 0.3-0.9). In a study of ~300 Koreans, rs25487(A;G) and (G;G) genotypes had an approximately 2-fold increased risk of basal cell cancer compared to rs25487(A;A) individuals (adjusted odds ratio 2.324, CI: 1.11-4.86, respectively).
48.3	rs653178 (A;G)

			This SNP, rs653178, is basically a proxy (r²>0.99) for rs3184504, as both are associated with celiac disease; see rs3184504 for more details.
48.3	rs601338 (A;G)	normal response to Norwalk

			rs601338 is found chromosome 19 in the gene FUT2 and the rs601338(G;G) confers genetic immunity to Norwalk virus (PMID 12692541)
48.3	rs363043 (C;C)	normal IQ

			This is one of four SNPs in the first intron of the SNAP25 gene that have been correlated with increased intelligence based on studies of ~300 Caucasian subjects. The (T;T) genotype averages several PIQ points higher than the (C;T) genotype, which averages several PIQ points higher than the (C;C) genotype. For SNPs rs363039 - rs363043 - rs353016, respectively, the haplotype C-T-T is most associated with higher intelligence in children, whereas the haplotype C-C-T is most associated in adults (SNPs oriented as in dbSNP).
48.3	rs669 (A;G)	possibly increased risk for Alzheimers

			rs669 is a SNP in the alpha-2-macroglobulin A2M gene. In dbSNP orientation, the rs669(A) allele encodes an isoleucine, and the rs669(G) allele encodes a valine; the SNP is also known as the Ile/Val variant. On its own, rs669 was not seen to reprocudibly and independently increase risk for Alzheimer's disease in several studies of ~200 Italian patients. However, the T-C-A haplotype of rs12316150-rs1050283-rs669 was associated with both early- and late-onset Alzheimer's disease. The majority of the disease risk from this haplotype was based on rs1050283. The original 2004 study of 148 Italian sporadic AD patients yielded an odds ratio for the rs669(G;G) genotype (as oriented in dbSNP orientation) of 3.81 (CI: 1.66-8.75). The presence of rs2333227(C;C), in addition to rs669(G;G), appears to s...
48.3	rs11362 (G;G)	normal risk

			Heterozygotes for SNP rs11362, located in the DEFB1 gene, are reported to be at increased risk for colonic Crohn's disease - but not the ileal or ileocolonic forms of the disease - based on a study of 190 Caucasians. The odds ratio is 2.393 (CI: 1.18-4.87, p=0.02).
48.3	rs707284 (A;G)

			linked to schizophrenia with rs7598440, rs839523, and rs707284
48.3	rs9739493 (C;T)	higher risk for hypertension

			rs9739493, a SNP in the KIAA0789 gene, was associated with risk for hypertension in a study involving 1,500+ Japanese patients. The odds ratio associated with the risk allele, rs9739493(T), was not directly reported. Note that another SNP in the KIAA0789 gene, rs3794260, was determined to be in a different linkage disequilibrium block, and is thus thought to be an independent risk factor for hypertension.
48.3	rs3900940 (T;T)	normal

			rs3900940 is a SNP in the MYH15 gene. The risk allele in terms of heart disease is rs3900940(C). This SNP is one of the 5 used by Celera's genetic risk score (GRS) for coronary heart disease (CHD). rs20455, in the KIF6 gene rs3900940, in the MYH15 gene rs7439293, in the PALLD gene rs2298566, in the SNX19 gene *rs1010, in the VAMP8 gene For each of the five variants, the GRS was increased by 1 if the subject was homozygous for the risk variant, unchanged if heterozygous, and decreased by 1 if the individual did not carry the variant. Therefore, individuals carrying all 10 possible risk variants (two copies of each of the five SNPs) were assigned a GRS of 5 and those carrying no risk variants a GRS of -5. A high GRS was defined as 3 or higher. Approximately 4% of the white cohort in ARIC...
48.3	rs5015480 (C;T)

			associated with type-2 diabetes
48.3	rs997669 (A;G)	?

			rs997669 shows an association with breast cancer in a British study involving ~2300 patients. The odds ratio for the (G;G) vs (A;A) homozygotes is 1.18 (CI: 1.04-1.34, p=0.003).
48.3	rs1303 (G;T)

			[omim:PI M3]
48.3	rs203462 (A;G)

			Linked to breast cancer [omim:LONGEVITY, REDUCED]
48.3	rs3184504 (C;T)	increased risk for celiac disease

			rs3184504 is a nonsynonymous SNP in the SH2B3 gene, and it is also known as R262W. In a recent (2008) study of non-HLA SNP associations of 1600+ celiac disease patients, this SNP was considered one of the most significant. The odds ratio for the minor allele was 1.19 (CI:1.101.30, p=1.33x10e-7). rs653178, another SNP in strong linkage disequilibrium (r²>0.99) with rs3184504, was also associated with celiac disease. associated with type-1 diabetes
48.3	rs1111875 (A;G)	1.3x risk of [[type-2 diabetes]]

			rs1111875 is a SNP of the HHEX homeobox gene. In several studies, it has been associated with risk for type-2 diabetes (T2D). In a study of 500 unrelated Caucasian T2D patients, the rs1111875(G) allele was overrepresented; the odds ratio was 1.68 (CI: 1.19-2.35, p=0.003). In this population, the population attributable risk for this allele was estimated to be 36%. In a study of ~400 Japanese, rs1111875(G) was also associated with type-2 diabetes (odds ratio 1.42, CI: 1.13-1.78, p=0.0024). Heterozygous and homozygous carriers of the risk allele had odds ratios of 1.31 (CI: 0.97-1.77, p=0.0810) and 2.40 (CI: 1.34-4.32, p=0.0028) relative to non-carriers. And in a third study, 1,630 Japanese patients were also found to have this SNP significantly overrepresented (p=0.0064). 1,638 type 2 diabe...
48.3	rs5174 (A;G)	1.3x increased risk for heart disease

			rs5174 encodes a variant of the LRP8 gene, encoding the low density lipoprotein receptor-related 8 protein (or the apolipoprotein e receptor). The variant affects the protein, changing an arginine to a glutamine; depending on the publication, it can be referred to by terms like R952Q or Arg952Gln. In three Caucasian populations combined, the odds ratio for coronary artery disease or myocardial infarction (and thus heart disease) is 1.31 (adjusted p=0.0003). Note that this association was only seen in populations with familial and premature disease, as a study of 1,231 patients with primarily late-onset, sporadic heart disease did not show any correlation with this SNP.
48.3	rs10260404 (C;T)	1.2x risk for ALS

			rs10260404, a SNP in the region of the DPP6 gene on chromosome 7, has been associated with the sporadic form of ALS (Lou Gehrig's disease) in a study of 1000+ European patients. The overall odds ratio for the risk allele rs10260404(C) is 1.30 (CI: 1.18-1.43, p=0.017). When broken down by genotype, the odds ratios for heterozygotes are 1.20 (CI: 1.06-1.41), and for rs10260404(C;C) homozygotes, 1.60 (CI: 1.32-1.92). A 'CC' haplotype for this SNP and that of it's neighbor rs10239794 is also highly (statistically; p=10e-9) associated with ALS.
48.3	rs2593813 (T;T)

			Category:is a snp [http://cat.inist.fr/?aModele=afficheN&cpsidt=16815755] Homozygosity for the rs2593813:G-rs4917:Met-rs4918:Ser haplotype conferred an increased risk for leanness
48.3	rs737865 (T;T)

			part of a three marker haplotype rs737865-rs4680-rs165599 COMT haplotypes at rs737865 and rs165599 may predict a favorable outcome for bupropion treatment for smoking cessation. We have typed the IVS 1 rs737865 and 3' rs615599 sites and also included a novel IVS 1 indel polymorphism. We report that the schizophrenia-associated haplotype is significantly heterogeneous in populations worldwide. may affect non-Hodgkin lymphoma, anxiety-related personality traits Also mentioned in these PMIDs * * * * * *
48.3	rs1935881 (A;G)

			Left atrial size, rs1935881 (FAM5C, p = 6.56*10(-6));
48.3	rs2107301 (C;C)	normal risk

			rs2107301 is a SNP in the vitamin D VDR receptor gene. rs2107301(T;T) homozygotes were associated with an ~2.5x higher risk of prostate cancer compared to homozygote carriers of the more common (C) allele in the 630 Caucasian patients studied.
49.1	rs351855 (C;T)	?

			The Arg form of this snp is likely to cause a hard to treat version of breast cancer. It determines the efficacy of Herceptin. This is the snp described in as the FGFR4-Gly388Arg mutation. [omim:CANCER PROGRESSION AND TUMOR CELL MOTILITY]
49.2	rs734232 (A;G)

			rs734232 has been reported in to be associated with psoriasis in a study of US psoriasis patients. However, the results of another study failed to support rs734232 as a psoriasis susceptibility factor in German psoriasis patients.
49.2	rs10246939 (C;T)	can taste bitter

			rs10246939 is one of three SNPs that form the main haplotypes behind the ability to perceive as bitter the taste of the compound phenylthiocarbamide (PTC) and similar molecules in foods (like cabbage and raw broccoli) or drinks (like coffee and dark beers). The rs10246939(C) allele, in the orientation shown in dbSNP, is the 'tasting' allele, and it is dominant to the 'non-tasting' allele rs10246939(T), so having one copy is enough to have the bitter tasting ability. If you are a 'taster', you're also likely to carry at least one rs713598(G) and one rs1726866(C) allele since, along with rs10246939(C), these three SNPs form the most common tasting haplotype. If you lack these alleles, you're quite likely (~80%) to be a non-taster of bitterness, meaning that foods that may taste bitter to oth...
49.2	rs2773080 (C;T)

			Associated with type-2 diabetes in a Mexican-American population.
49.2	rs17696736 (A;G)	1.3x risk

			rs17696736 has been reported in a large study to be associated with type-1 diabetes. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.34 (CI 1.16-1.53), and for homozygotes, 1.94 (CI 1.65-2.29). In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for this SNP was recalculated to be 1.22 (CI 1.151.28).
50.0	rs12896399 (G;T)

			[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000074 plos] associated with hair color rs12896399 rs12203592
50.0	rs726601 (C;C)	normal

			rs726601 is among several SNPs in the SORL1 gene that show some association with increased (or decreased) risk for Alzheimer's disease in a study of 1,400 Caucasians.
50.0	rs1050828 (G;G)

			[omim:G6PD ASAHI]
50.0	rs2285644 (C;C)

			[omim:DIEGO BLOOD GROUP ANTIGEN]
50.0	rs4880 (C;T)

			The rs4880(T) allele, part of the codon for amino acid valine at codon 16 of the antioxidant protein from the mitochrondrial superoxide dismutase 2 SOD2 gene, is the most common in most populations studied. The rs4880(C) allele gives rise to an alanine at this position. There appears to be some conflict in the literature over the effect of this SNP. Having a valine at codon 16 is said to reduce enzyme activity , and thus lead to increased oxidative stress, yet in at least one study of the actual enzyme levels measured in people, SOD2 activity was 33% higher in (C;T) or (T;T) individuals compared to (C;C) individuals . Regardless of how this resolves, several phenotypic associations have been reported for this SNP, including: * A 10 fold higher risk for heart disease in hereditary hemochrom...
50.0	rs3738401 (G;G)

			rs3738401 is a SNP in the DISC1 gene, known as R264Q. Associated with schizophrenia 13 single-nucleotide polymorphisms (SNPs) in 723 members of 179 Finnish Bipolar disorder families. rs751229(T) and rs3738401(A) was over-transmitted to males with psychotic disorder. under-transmitted rs821616(T) and rs1411771(T) *The risk haplotype for psychotic disorder also associated to perseverations (P = 0.035; for rs751229 alone P = 0.0012), and a protective haplotype G-T-G with rs1655285 in addition to auditory attention (P = 0.0059).
50.0	rs1041983 (C;C)

			rs1041983 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1041983(T).
50.0	rs1726866 (C;T)	can taste bitter

			rs1726866 is one of three SNPs that form the main haplotypes behind the ability to perceive as bitter the taste of the compound phenylthiocarbamide (PTC) and similar molecules in foods (like cabbage and raw broccoli) or drinks (like coffee and dark beers). The rs1726866(C) allele is the 'tasting' allele, and it is dominant to the 'non-tasting' allele rs1726866(T), so having one copy is enough to have the bitter tasting ability. If you are a 'taster', you're also likely to carry at least one rs713598(G) and one rs10246939(C) allele since, along with rs1726866(C), these three SNPs form the most common tasting haplotype. If you lack these alleles, you're quite likely (~80%) to be a non-taster of bitterness, meaning that foods that may taste bitter to others taste far less bitter to you.
50.8	rs646776 (A;A)

			rs599839 and rs4970834 explain about 1% of the variation in circulating LDL-cholesterol levels. 'When we look at this particular genetic variance, of all the cholesterol variation among the population, 1% of it can be attributed to this particular locus,' said Sandhu. 'This is equivalent to more established genes for LDL regulation, particularly APOE.' rs646776 also linked.
50.8	rs3087243 (A;G)	increased risk for auto-immune diseases

			The rs3087243 SNP is also known in the literature as the CT60 G>A or the +6230G>A polymorphism, and it is located in the CTLA4 gene. In Asian (Japanese) populations, the presence of an rs3087243(G) allele represents a 1.3 fold increased risk of autoimmune thyroid disease, and for those with autoimmune thyroid disease, a 1.5 fold increased risk of type-1 diabetes. However, in individuals without autoimmune thyroid disease, no association was seen between this SNP and type-1 diabetes. The authors speculate that earlier studies may have reported associations between this SNP and type-1 diabetes that were actually primarily based on the association with autoimmune thyroid disease. This same SNP, rs3087243, has also been implicated as a (minor) risk factor for developing rheumatoid arthritis (...
51.7	rs725613 (A;A)

			associated with type-1 diabetes
51.7	rs5882 (A;A)

			[omim:LONGEVITY, EXCEPTIONAL]
51.7	rs6910071 (A;A)	0 dose of HLA-DRB1*0401

			This SNP, along with SNPs rs660895 and rs3817964, is a tag SNP for the HLA-DRB10401 allele. The HLA-DRB10401 allele has been associated with higher risk for rheumatoid arthritis, and in particular, rheumatoid vasculitis. The association is seen particularly for individuals carrying two copies of, i.e. homozygous for, the allele. The reported odds ratio for rs6910071(G;G) homozygotes is 6.2 (CI: 1.01 - 37.9). The risk for rheumatoid arthritis may be higher for individuals carrying one copy (one 'dose') of the HLA-DRB10401 allele, if they also carry a different HLA-DRB1 risk allele. In particular, 0401/0404 individuals are reported to have an odds ratio for rheumatoid vasculitis of 4.1 (CI: 1.1 - 16.2), and 0401/*0101 individuals have an odds ratio of 4.0 (CI: 1.4 - 11.6).
51.7	rs2305767 (A;G)

			rs2305767 (P = 1.16 x 10(-4); OR 1.41, 95% CI 1.18-1.67). We demonstrate significant association of allelic variants in MYO9B with schizophrenia
51.7	rs3803662 (C;C)	normal

			rs3803662, a SNP associated with the TNRC9 gene, was one of the four strongest associating SNPs found in a genome-wide association study of over 4,000 breast cancer samples. rs3803662(T;T) have a 1.64-fold greater risk of estrogen receptor-positive tumors In a study of 1,267 breast cancer patients, rs3803662 heterozygote carriers and minor allele homozygote carriers were more likely to be diagnosed before the age of 60 years (p = 0.025) relative to major allele homozygote carriers. breast cancer *rs2981582, rs3803662, and rs889312) showed weak but significant associations with ER-negative disease, the strongest association being for rs3803662 in TNRC9 (1.14 (1.09-1.21))
51.7	rs1004819 (C;C)	common

			SNP rs1004819, in the IL23R gene, is associated with increased risk for Crohn's disease in both Jewish and non-Jewish populations. The same risk allele is also reported to increase the risk for developing ankylosing spondylitis, based on a large study of over 1,000 Caucasian patients. The odds ratio is 1.2 (p=8.8x10e-5).[PMID 17952073, PMID 18037607] significant associations with rs1004819, rs7517847, and rs11209026. Having any CARD15 variant was associated with a significant risk for CD (P < 0.0001).
51.7	rs1800469 (C;C)	higher risk for COPD

			rs1800469, a SNP in the promoter region of the transforming growth factor beta1 TGFB1 gene has been associated with increased risk for chronic obstructive pulmonary disease (COPD). Although smoking is the main risk factor, smokers with a rs1800469(C) allele (or 2 other TGFB1 SNPs, rs1982073 and rs2241712) were more likely to develop COPD, based on a study of ~700 Caucasian subjects
51.7	rs2234036 (G;G)

			[omim:THYROXINE-BINDING GLOBULIN, VARIANT A]
51.7	rs144848 (G;T)

			This SNP, a variant in the BRCA2 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (G). [omim:BREAST CANCER, TYPE 2, SUSCEPTIBILITY TO]
51.7	rs4464148 (T;T)	1x normal risk for colorectal cancer

			rs4464148 is one of 3 SNPs in the SMAD7 gene associated with risk for colorectal cancer, based on a large study (7,400+ cases) conducted in the UK. The odds ratios show an increased risk for the minor rs4464148(C) allele; the OR for (C;C) homozygotes is 1.35 (CI: 1.2-1.51), and for (C;T) heterozygotes 1.10 (CI: 1.09-1.21), overall p=7x10^-8.
51.7	rs660895 (A;G)	1 dose of HLA-DRB1*0401

			This SNP, along with SNPs rs6910071 and rs3817964, is a tag SNP for the HLA-DRB10401 allele. The HLA-DRB10401 allele has been associated with higher risk for rheumatoid arthritis, and in particular, rheumatoid vasculitis. The association is seen particularly for individuals carrying two copies of, i.e. homozygous for, the allele. The reported odds ratio for rs660895(G;G) homozygotes is 6.2 (CI: 1.01 - 37.9). The risk for rheumatoid arthritis may be higher for individuals carrying one copy (one 'dose') of the HLA-DRB10401 allele, if they also carry a different HLA-DRB1 risk allele. In particular, 0401/0404 individuals are reported to have an odds ratio for rheumatoid vasculitis of 4.1 (CI: 1.1 - 16.2), and 0401/*0101 individuals have an odds ratio of 4.0 (CI: 1.4 - 11.6).
51.7	rs3817198 (C;T)

			rs3817198, a SNP associated with the LSP1 gene, was one of the four strongest associating SNPs found in a genome-wide association study of over 4,000 breast cancer samples.
51.7	rs6502867 (T;T)

			linked to generalized vitiligo Individuals carrying high-risk alleles of both rs6502867 and rs2670660 had an odds ratio of 4.20 compared with individuals carrying a high-risk allele from only one signal.
52.5	rs2278206 (T;T)	1.16x increased risk for asthma

			A study of ~170 families led to a slight association between rs2278206 and atopic asthma. The risk genotype - in dbSNP orientation, not as published - is rs2278206(T;T). Conversely, the rs2278206(C;C) genotype was rarely (odds ratio 0.13) seen in patients with atopic asthma.
52.5	rs7501939 (C;T)

			[http://www.cancerpage.com/news/article.asp?id=11059] related to Prostate cancer and Type-2 diabetes [http://cancergenetics.wordpress.com/2008/02/15/prostate-cancer-oldnew-snps-and-decodeprca/ cancer-genetics] these snps influence genetic risk for prostate cancer the haplotype rs6983267 rs1016343 rs4242384 rs7501939 rs1859962 rs2660753 rs9364554 rs6465657 rs10993994 rs7931342 rs2735839 rs5945619 *rs10993994
52.5	rs419598 (T;T)
			One report indicates that rs419598(T;T) carriers, if they are also IL1B -511 heterozygotes, have an increased chance of surviving a bout of bacterial meningitis . The (T;T) genotype is the most common in all populations studied.
			May modulate other variations. IL1B -511 allele heterozygotes have a 4 fold higher chance of surviving bacterial meningitis than (either) homozygote . Odds of surviving meningitis apparently further increase 2X for IL1B -511 heterozygotes who are also rs419598(T;T), i.e. homozygous for IL1RN +2018 rs419598 (T) allele (the most common one; also known as '+8006').
52.5	rs13277113 (G;G)

			Associated with systemic lupus erythematosus (SLE)
52.5	rs1799929 (C;T)

			rs1799929 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1799929(T).
53.3	rs1799930 (G;G)

			rs1799930 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1799930(A).
53.3	rs10889677 (C;C)	1x risk for certain autoimmune diseases; 2.3x risk for Graves disease

			SNP rs10889677, in the IL23R gene, is associated with increased risk for Crohn's disease in both Jewish and non-Jewish populations. The same risk allele for this SNP has been associated with increased risk for ankylosing spondylitis in a large study of over 1,000 Caucasian patients. The odds ratio is 1.3 (p=1.3x10e-6).[PMID 17952073, PMID 18037607] In a study of 216 North American patients with Graves' disease, the C allele of rs10889677 was 2.03x overrepresented (p=1.3x10⁴), and the homozygous rs10889677(C;C) genotype was also overrepresented (2.36x; p=1.4x10^-4) in Graves ophthalmopathy patients.
53.3	rs2156921 (A;G)	1.3x increased risk for depression

			rs2156921, a SNP in the BCR gene on chromosome 22, has been associated with increased risk for depression. The odds ratio for carriers of the minor allele (G) are reported as 1.29 (p=0.031) based on a study of 329 Japanese patients.
53.3	rs11149566 (A;A)

			Suspected of reproducibility problems based on [http://www.kk.org/quantifiedself/2008/05/testing-genetic-test-chips.php end user analysis] rs11149566 rs4458717 rs4660646 rs754499
53.3	rs4402960 (G;G)

			associated with type-2 diabetes significantly associated with type-2 diabetes p = 0.00009; in 1,630 Japanese subjects and in 1,064 controls 1,638 type 2 diabetes patients and 1,858 controls *rs4402960 borderline (OR 1.10, 95% CI: 0.99-1.22).
53.3	rs1859962 (G;T)	normal risk
			This is the genotype of User:Watson
			rs1859962 is a SNP on chromosome 17q24.3, associated with increased risk for prostate cancer in several studies. In a study of over 3,600 Caucasians with prostate cancer, rs1859962 is one of five SNPs used (with family history as a sixth factor) to cumulatively predict overall risk. On its own, the rs1859962(G;G) risk genotype yields an odds ratio for developing prostate cancer of 1.28 (CI: 1.11-1.47, p=5.5x10e-4) and may account for 6.5% of population attributable risk. [http://www.cancerpage.com/news/article.asp?id=11059 news] linked to Prostate cancer and type-2 diabetes [http://cancergenetics.wordpress.com/2008/02/15/prostate-cancer-oldnew-snps-and-decodeprca/ cancer-genetics] these snps influence genetic risk for prostate cancer the haplotype rs6983267 rs1016343 rs4242384 rs7501939 ...
53.3	rs1709183 (A;A)

			rs1709183 associated with EDV endothelium-dependent vasodilation in resistance, but not conduit arteries
53.3	rs977785 (C;C)	increased risk

			rs977785, a SNP purported to be in the promoter of the LY86 gene, is reported to be associated with mite-sensitive allergies in children, based on a study of 500+ Taiwanese patients. The allele that is underrepresented (and thus protective?) is the minor allele, which in dbSNP orientation is rs1334710(A).
53.3	rs3753394 (C;C)

			linked to blindness in old age rs3753394 carries a significantly increased risk for exudative AMD. linked to rs3753394, rs800292, rs1061147, rs1061170, rs380390, and rs1329428 Significant associations were detected for AMD with rs3753394 rs800292 rs1329428 A haplotype of rs1061170 rs3753394 rs800292 rs1329428 (TGTC) was found to confer a significantly increased likelihood of exudative AMD CFH variations appear to contribute to ARMD in Caucasians, but not in Japanese
53.3	rs1360780 (C;C)	normal

			In Caucasian non-Hispanics, the rs1360780(T) allele is associated with increased risk for depression, with an odds ratio of 1.39 (CI: 1.14-1.70, p=0.046). This same SNP, which is in the FKBP5 gene, may influence how patients respond to antidepressants including citalopram. rs1360780(T;T) homozgyotes tend to report more depressive episodes, but they also respond better to treatment with antidepressants. rs9296158 rs3800373 rs1360780 rs9470080 linked with the severity of child abuse to predict level of adult PTSD symptoms after correcting for multiple testing.
53.3	rs1470579 (A;A)

			T2D and normal glucose tolerant (NGT) individuals. (3,295 T2D and 3,595 NGT), strong associations with T2D were found for CDKAL1 (OR(rs7756992) = 1.30[1.19-1.42], P = 2.3x10(-9)) CDKN2A/2B (OR(rs10811661) = 0.74[0.66-0.82], P = 3.5x10(-8)) *IGFBP2 (OR(rs1470579) = 1.17[1.07-1.27], P = 0.0003) SNPs. T2D risk increased strongly when risk alleles, including the previously discovered T2D-associated TCF7L2 rs7903146 SNP, were combined (8.68-fold for the 14% of French individuals carrying 18 to 30 risk alleles with an allelic OR of 1.24)
53.3	rs10508266 (G;G)

			rs10508266 and rs3750861 near KLF6 shows significant association with Lung cancer risk.
53.4	rs2070045 (T;T)

			SNP rs2070045, a variant of the SORL1 gene, has been reported to be associated with Alzheimer's disease. However, a subsequent study of over 2,000 patients found a weak (at best) association.
53.4	rs13551 (A;A)

			[omim:FU1/FU2 POLYMORPHISM]
53.4	rs8089 (T;T)	normal risk

			rs8089, a SNP in the thrombospondin-2 THBS2 gene, was studied as part of a large study (>5,000 Caucasian patients) for risk of myocardial infarction and thus heart disease. Although statistically not overwhelming, a risk was seen (odds ratio 1.19, CI: 1.02-1.39, compared to (T;T) homozygotes) for carriers of the less common rs8089(G) allele. In a meta-analysis combining several studies, no statistically significant association for heart attacks was seen for rs8089, nor for that matter, 2 other SNPs, rs2228262 (also known as Asn700Ser) or rs1866389 (also known as Ala387Pro), in thrombospondins -1 and -4, respectively.
54.2	rs228591 (C;T)

			rs8178085 and rs12334811 with approaching dose-dependent effect on lung cancer predisposition, subjects carrying two to four risk genotypes were associated with a 43% decreased lung cancer risk compared with subjects carrying zero to one risk genotypes (adjusted odds ratio, 0.53; 95% confidence interval, 0.35-0.80). rs228591 variant allele or ataxia-telangiectasia and Rad3-related rs6782400 wild-type homozygous genotype
55.0	rs299290 (T;T)

			[http://cancergenetics.wordpress.com/2007/10/13/exciting-discoveries-of-2007-breast-cancer/ cancergenetics] The risk of breast cancer was 23% higher in women who had one copy of genetic variant (the A-C-A haplotype: rs7712023-rs299290-rs10515860), and 46% higher in women with two copies. In addition, those women were diagnosed an average of 12 months younger than women from the control group, suggesting that HMMR is linked to early-onset breast cancer.
55.0	rs757863 (A;G)

			This SNP was associated with amyotrophic lateral sclerosis (ALS) based on a study of 1,152 patients.
55.0	rs20455 (C;T)	increased risk of coronary heart disease; better response to statins

			rs20455, often called Arg719, is a reasonably well studied SNP in the KIF6 gene. The risk allele (encoding the arginine at position 719) is rs20455(C). This SNP is one of the 5 used by Celera's genetic risk score (GRS) for coronary heart disease (CHD). rs20455, in the KIF6 gene rs3900940, in the MYH15 gene rs7439293, in the PALLD gene rs2298566, in the SNX19 gene *rs1010, in the VAMP8 gene For each of the five variants, the GRS was increased by 1 if the subject was homozygous for the risk variant, unchanged if heterozygous, and decreased by 1 if the individual did not carry the variant. Therefore, individuals carrying all 10 possible risk variants (two copies of each of the five SNPs) were assigned a GRS of 5 and those carrying no risk variants a GRS of -5. A high GRS was defined as 3 ...
55.0	rs4807015 (C;T)

			rs1143699, rs4807015, and rs1978237 confer an increased risk of developing type-2 diabetes
55.0	rs6908425 (C;C)	1.9x risk

			rs6908425 has been reported in a large study to be associated with Crohn's disease. The risk allele (oriented to the dbSNP entry) is (C); the odds ratio associated with heterozygotes is 1.63 (CI 1.38-2.25), and for homozygotes, 1.95 (CI 1.43-2.67).
55.0	rs2073711 (C;C)	higher risk of LDD

			A study of Asian patients with lumbar disc disease (LDD) implicates each copy of a (C) allele of SNP rs2073711 (as oriented with respect to dbSNP) as increasing risk about 1.6 fold. [omim:LUMBAR DISC DISEASE, SUSCEPTIBILITY TO]
55.0	rs2201841 (T;T)	2.4x risk for Graves' disease

			SNP rs2201841, in the IL23R gene, is associated with increased risk for Crohn's disease in both Jewish and non-Jewish populations. Another study found that the 'A allele' and 'AA genotype' were significantly overrepresented in Graves' disease patients with Graves ophthalmopathy, based on 216 North American patients. The odds ratios reported were 2.04 for the allele (p=1x10^-4), and for the so-called 'AA' genotype (presumably rs2201841(T;T) when correctly oriented to the dbSNP orientation), 2.4 (p=1x10^-4).
55.0	rs6332 (A;G)

			Adult attention deficit hyperactivity disorder (ADHD) 143 high-risk male subjects . rs6332 showed a trend toward an association between the A-allele and increased scores
55.0	rs7997012 (A;G)	normal risk

			rs7997012, located in an intron of the HTR2A gene, was found to be associated with a somewhat increased rate of successful response to treatment of depression with the drug citalopram. From this article : 'HTR2A encodes the serotonin 2A receptor, which is downregulated by citalopram. Participants who were homozygous for the A allele had an 18% reduction in absolute risk of having no response to treatment, compared with those homozygous for the other allele.' * See also [http://www.anxietyinsights.info/antipressant_effectiveness_predicted_by_gene_variation.htm Anxiety Blog] posting
55.2	rs1053049 (T;T)

			rs1053049, rs6902123, and rs2267668 in PPARD affect Lifestyle Intervention induced changes in overall adiposity, hepatic fat storage, and relative muscle mass. Our findings provide a mechanistic explanation for the involvement of these genetic variations in the development of insulin resistance and type-2 diabetes.
55.6	rs1800278 (A;A)

			[omim:DUCHENNE MUSCULAR DYSTROPHY]
55.9	rs7901695 (T;T)

			implicated in type-2 diabetes according to this [http://thegenesherpa.blogspot.com/2007/08/tcf7l2-strikes-again-this-time-its.html Gene Sherpas post]
55.9	rs235326 (C;C)

			651 people of Japanese ethnicity, of which 274 were Japanese Americans living in Hawaii, and the remaining 377 were native Japanese. In the Japanese-American population, the risk of obesity was found to be 3.29-fold higher (a 95% confidence interval of 1.25-8.67, P = 0.02) in TT homozygotes than in C carriers. associated with obesity in Japanese living in the United States whose diet has become 'westernized.'
55.9	rs17070145 (C;C)	normal form

			In a Swiss cohort: 'Carriers of KIBRA rs17070145 T allele had 24% better free recall performance 5 min after word presentation (P = 0.000004) and 19% better free recall performance 24 hours after word presentation (P = 0.0008) than did noncarriers.' In a US cohort: 'T allele carriers had significantly better memory scores than non-carriers in the Buschke's Selective Reminding Test (SRT). Performance on another episodic memory task, the Rey Auditory Verbal Learning Test (AVLT), was also significantly different between allele groups.' In another Swiss cohort, with a visual episodic memory task: 'T allele carriers also performed significantly better than did noncarriers in this population.' 'Functional magnetic resonance imaging detected KIBRA allele-dependent differences in hippocampal activ...
55.9	rs3771150 (C;C)

			This SNP was associated with amyotrophic lateral sclerosis (ALS) based on a study of 1,152 patients.
55.9	rs3129934 (C;C)

			associated with type-1 diabetes
56.7	rs1044471 (C;T)

			g.-7309A>G (rs75172865) associated with lower insulin resistance and reduced the promoter activity.g.33447T (rs1044471) associated with smaller waist circumference
56.7	rs326 (A;A)	lower HDL cholesterol

			The (A) allele of rs326 was associated with risk for lower high-density lipoprotein (HDL) cholesterol plasma levels in 3 independent population samples, including both Caucasians and African-Americans.
56.7	rs1800588 (C;C)

			rs1800588, also known as the -514C/T polymorphism of the LIPC gene, may influence the levels of the 'good' cholestorols, the high density lipoprotein (HDL) cholesterols. Generally, the (T) allele (as published) is considered to lead to higher HDL levels. However, high HDL cholesterol, at least when combined with another HDL raising SNP (rs708272), doesn't appear to actually protect individuals from coronary artery disease, at least based on one study of ~800 Caucasian male patients. [PMID 18164013
56.7	rs5370 (G;G)

			[http://www.genome.jp/dbget-bin/www_bget?omim+131240 omim 131240] In a study of 103 candidate genes for coronary artery disease and associated phenotypes in the founder population of the Saguenay Lac St-Jean region of Quebec, Pare et al. (2007) found that HDL cholesterol levels were associated with a lysine-to-asparagine substitution at codon 198 (K198N) of the EDN1 gene in a sex-specific manner. The minor allele T (asn) of the K198N substitution (dbSNP rs5370) was associated with lower HDL cholesterol values. Women showed a strong association between dbSNP rs5370 and HDL cholesterol (P = 1.3 x 10(-5)), whereas in men no such significant association was identified (P = 0.14).
56.7	rs6897932 (C;C)	increased risk multiple sclerosis

			The (C) allele of rs6897932, located in the alternatively spliced exon 6 of IL7RA gene and encoding the amino acid threonine rather than isoleucine at amino acid position 244, is associated with a slight increase (18%) in risk of developing multiple sclerosis. [PMID 17660817; Nature Genetics 39, 1083 - 1091 (2007) SG Gregory et al.] Note that the (C) allele is the most common at this position in all known populations and influences the ratios of the alternative isoforms (membrane bound and soluble) of the gene. [http://thegenesherpa.blogspot.com/2007/07/ms-genes-and-gwas.html blog post] giving perspective on the significance of this snp a significant risk factor for multiple sclerosis in four independent (overall P = 2.9 x 10(-7)) influences the amount of soluble and membrane-bound isofor...
56.7	rs2070762 (C;T)

			association with essential hypertension . Functional analysis showed that the C allele of rs2070762 functioned as an enhancer in the absence of binding by unidentified transcriptional repressor(s)
56.7	rs7598440 (C;T)

			linked to schizophrenia with rs7598440, rs839523, and rs707284
56.7	rs7946 (T;T)

			rs7946, a SNP in the phosphatidylethanolamine N-methyltransferase PEMT gene and also known as +5465G-A, leads to a V175M (valine to methionine at amino acid position 175) substitution in the PEMT protein, and is a loss of function mutation. Caucasians with nonalcoholic fatty liver are more likely to carry the rs7946 (A), with the effect being most pronounced for rs7946(A;A) genotypes. However, rs7946(A) carriers are not more likely to have fatty liver, based on a study of many more patients, including ones of Hispanic and African-American descent. How can this be? One explanation [doi: 10.1096/fj.06-1005ufm] concludes the following: * Caucasians have a different distribution of this SNP than do Hispanics and African Americans; * Having this SNP may be necessary, but is not sufficient, to...
56.7	rs3212227 (A;A)

			IL12B gene SNP, part of a haplotype with rs6887695 associated with psoriasis.
56.7	rs1800497 (C;C)	A2/A2 [[bupropion]] effective

			rs1800497, a SNP also known as the TaqIA (or Taq1A) polymorphism of the dopamine D2 receptor DRD2 gene (even though it is actually located over 10,000bp downstream of the gene), gives rise to the DRD2*A1 allele. This allele (rs1800497(T)) is associated with a reduced number of dopamine binding sites in the brain , and has been postulated to play a role in alcoholism, smoking, and certain neuropsychiatric disorders. The reduced number of dopamine binding sites may play a role in nicotine addiction by causing an 'understimulated' state that can be relieved by smoking (and/or use of other drugs). A wide variety of reports have been published over more than ten years either linking rs1800497 to aspects of nicotine use and smoking cessation success, or finding no such association. A meta-analy...
56.7	rs4430796 (A;G)	normal risk

			rs4430796 is a SNP in the TCF2 gene on chromosome 17q12, associated with increased risk for prostate cancer in several studies. In a study of over 3,600 Caucasians with prostate cancer, rs4430796 is one of five SNPs used (with family history as a sixth factor) to cumulatively predict overall risk. On its own, the rs4430796(A;A) risk genotype - in dbSNP orientation, not as published - yields an odds ratio for developing prostate cancer of 1.38 (CI: 1.21-1.57, p=1.6x10e-6) and may account for 10.2% of population attributable risk. [http://www.cancerpage.com/news/article.asp?id=11059] linked to Prostate cancer and type-2 diabetes
56.7	rs7520974 (A;G)

			associated with specific patterns of brain activity. rs3087454 rs1355920 rs7520974 rs885834
56.7	rs3135388 (C;C)

			Source [http://www.nature.com/ng/journal/v38/n10/fig_tab/ng1885_T1.html nature] rs3135388 is highly (> 99%) correlated with the HLA-DRB11501 allele, and it's risk allele (T) is associated with a 3 to 6 fold higher risk for developing multiple sclerosis. It has also been associated with other autoimmune diseases, such as SLE. Note that the HLA-DRB11501 allele is fairly common; for example, it occurs in 15-30% of most individuals of Northern European origin.
56.7	rs1800629 (G;G)	complex; generally normal risk

			rs1800629 is also known as the TNF -308 SNP, and occasionally the rs1800629(A) allele is referred to as 308.2 or TNF2 (with the more common (G) allele being 308.1 or TNF1). The (A) allele is associated with higher levels of TNF expression. This SNP has been linked to a wide variety of conditions: * A study of 108 Chinese patients concludes that rs1800629(A) carriers are at 3.23x (CI: 1.10-9.44) increased risk for liver cancer, and are also at higher risk for hepatic fibrosis and more severe liver damage. * A study of 120 Columbian patients with systemic lupus erythematosus found an increased risk for rs1800629(A) carriers (odds ratio 3.9, CI: 1.65-5.80, p= 0.0004). * A study of 600 Italian patients concluded that rs1800629(A) carriers are at increased risk for acute heart attacks and have ...
57.1	rs4970834 (C;C)

			rs599839 and rs4970834 explain about 1% of the variation in circulating LDL-cholesterol levels. 'When we look at this particular genetic variance, of all the cholesterol variation among the population, 1% of it can be attributed to this particular locus,' said Sandhu. 'This is equivalent to more established genes for LDL regulation, particularly APOE.' rs646776 also linked.
58.3	rs10050860 (C;C)	normal risk

			rs10050860 is one of several SNPs in the ARTS1 gene that has been shown in a large (over 1,000 Caucasian patients) study to be associated with ankylosing spondylitis. The odds ratio is 0.71 (p=7.7x10e-9).[PMID 17952073, PMID 18037607]
58.3	rs1815739 (C;T)	just right?

			This SNP, in the ACTN3 gene, encodes a premature stop codon in a protein likely to be important in muscle function. The polymorphism alters position 577 of the alpha-actinin-3 protein, and while the most common nucleotide at this position, (C), encodes an arginine (amino acid code R), the stop codon is refered to as X. Hence, the SNP is referred to as R577X, with homozygotes being either RR or XX and heterozygotes being RX. The main report studying a relatively small number of Australian elite (ie ~Olympic) athletes found that, at least in females, the R allele (ie rs1815739(C)) is associated with sprinters, while the X allele (rs1815739(T)) is associated with endurance athletes. No female or Olympic-level sprinters were XX homozygotes (rs1815739(T;T)). The association tended the same way ...
58.3	rs1550922 (A;G)

			SNP rs1550922 has been associated with both glucose levels and body-mass index (eg obesity) in the Framingham Heart Study datasets, and is thus associated with heart disease. [http://gmed.bu.edu/about/analysis.html source]
58.3	rs1801275 (A;A)

			[omim:ATOPY, SUSCEPTIBILITY TO]
58.3	rs231775 (A;G)

			rs231775 (CTLA4_+49_G/A P=0.0219) and rs733618 (CTLA4_-1722_T/C P=0.0096) susceptibility to Graves' disease associated with the development of placental abruption and preeclampsia, with women having the G allele being at risk [omim:HASHIMOTO THYROIDITIS, SUSCEPTIBILITY TO]
58.3	rs241447 (A;A)

			[omim:PEPTIDE TRANSPORTER PSF2 POLYMORPHISM]
58.3	rs241448 (T;T)	common

			While the ApoE4 allele (rs429358(C)) is widely accepted as the predominant genetic risk factor for Alzheimer's disease, there are likely to be numerous other factors, both genetic and environmental, associated to lesser degrees with susceptibility to the disease. Genes influencing the immune system, and in particular susceptibility to viral infections such as herpes, may be among such factors. This SNP, located in the TAP2 gene and thus implicated in the activation of HIV and HSV-1 viruses, is seen more commonly in ~300 Alzheimer patients than in the same number of controls. The risk allele is rs241448(C). The odds ratio is reported to be 2.14 (CI: 1.02-2.55) for rsrs241448(C;C) homozygotes, and 1.51 (CI: 0.80-1.93) for rsrs241448(C;T) heterozygotes, compared with rsrs241448(T;T) homozygo...
58.3	rs1379659 (A;A)

			Left ventricle diastolic dimension, rs1379659 (SLIT2, p = 1.17*10(-7))
59.3	rs7570682 (G;G)	normal

			rs7570682 has been reported in a large study to be associated with bipolar disorder. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.23 (CI 1.09-1.40), and for homozygotes, 1.64 (CI 1.28-2.12).
60.0	rs7216389 (C;T)	not clear

			rs7216389, a SNP in the ORMDL3 gene on chromosome 17q21, was associated with susceptibility to childhood asthma in a study of ~1,000 British patients. The variation appears to be linked to altered levels of the ORMDL3 mRNA, which was shown in a cohort study of ~5,000 British and German patients to be correlated to childhood asthma.
60.0	rs3741981 (C;T)

			Was investigated for a diabetes association, but seemed to have none. suggests it or a neighbor may be involved in multiple sclerosis
60.0	rs3803 (C;C)

			Category:needs help Category:interesting [http://genetics.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pgen.0020139 This paper] implicates this snp as playing a role in heart disease. Having a G at this position is considered normal. Having an A at this position reduces the risk of heart disease. Approximate 15% of all people carry this allele. '''Technical note:''' This applies to many other snps, but here is the first clean case I've encountered. dbsnp shows ss3839 and ss16241517 are being read 'fwd' ss16940640 and ss44449258 are being read in 'rev'. This has C/T alleles when read forward, and A/G when read in reverse. Since the authors of the paper above describe this as an A/G snp, it seems they are reading in reverse. Often papers include even less information, ...
60.0	rs11556045 (A;A)

			[omim:HEXB POLYMORPHISM]
60.0	rs1051931 (G;G)

			asthma related [omim:ASTHMA AND ATOPY, SUSCEPTIBILITY TO]
60.0	rs324420 (C;C)

			[omim:DRUG ADDICTION, SUSCEPTIBILITY TO]
60.0	rs8067378 (A;G)

			rs8067378 is the strongest associating SNP from a region of chromosome 17q21 found in a large (ultimately over 7,000 patients in 3 populations) genome-wide association study of childhood asthma. Since the associated SNPs were also strongly associated (p < 10^-22) in cis with transcript levels of from the ORMDL3 gene, the authors concluded that genetic variants regulating ORMDL3 expression are determinants of susceptibility to childhood asthma.
60.7	rs4714156 (C;C)	common

			rs4714156, a SNP located in the BTBD9 gene region, has been linked to a lower frequency of restless legs syndrome, a common sleep disorder, with an overall odds ratio of 0.61 (CI: 0.51-0.74) for the (T) minor allele.
61.7	rs1045642 (C;T)

			rs1045642, also known as C3435T, is a SNP located in the ABCB1 gene. It is often studied in conjunction with rs2032582. C3435T has been mentioned by: * (R)-lansoprazole (Prevacid) concentrations are significantly increased in CYP2C19 extensive metabolizers with ABCB1 C3435T C allele. * In a Korean population, plasma concentrations of fexofenadine (Allegra) were 17% lower in 2677AA/3435CC subjects and 47% higher in the 2677TT/3435TT subjects compared to 2677GG/3435CC subjects. * In contrast, in this study no association was observed between the C3435T polymorphism and fexofenadine plasma or urine concentrations in a German Caucasian population.
61.7	rs4961 (G;G)	normal

			rs4961 is a variation in the adducin 1 ADD1 gene, encoding a change from a glycine to a tryptophan, so it is also known as G460W. Originally, a study of 477 Italian patients indicated that carriers of one or two rs4961(T) alleles were at 1.8x increased risk for hypertension (CI: 1.32-2.43). This study also indicated that carriers of the risk (T) allele responded better to diuretics and sodium-restricted diets, in that they tended to lower their blood pressure by ~10 mmHg points compared to rs4961(G;G) homozygotes similarly treated. Subsequent studies have tended to confirm this association, and to extend it to risk for heart disease. They also have tended to confirm that risk allele carriers respond better to therapy. In a study of ~2200 Belgian patients, rs4961(T) carriers were generally ...
61.7	rs8055236 (G;G)	2.2x risk
			2.2x higher risk for heart disease
			rs8055236 has been reported in a large study to be associated with heart disease, in particular, coronary artery disease. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.91 (CI 1.33-2.74), and for homozygotes, 2.23 (CI 1.56-3.17).
61.7	rs2302762 (C;C)
			This is the genotype of User:Watson
			Variations in this snp have been linked to nicotine dependence
61.7	rs2286983 (C;C)

			SNP rs2286983 has been associated with both cholesterol levels and body-mass index (eg obesity) in the Framingham Heart Study datasets, and is thus associated with heart disease. [http://gmed.bu.edu/about/analysis.html source]
61.7	rs3732379 (C;C)

			[omim:HUMAN IMMUNODEFICIENCY VIRUS TYPE 1, RAPID PROGRESSION TO AIDS]
61.7	rs12913832 (G;G)	blue eye color, 99% of the time

			rs12913832 is a SNP near the OCA2 gene that may be functionally linked to blue or brown eye color, due to a lowering of promoter activity of the OCA2 gene. Blue eye color is associated with the rs12913832(G;G) genotype.[PMID 18172690, PMID 18252222] rs12913832 is also part of a haplotype spanning 166kB on chromosome 15, defined by 13 SNPs listed below, that is found in 97% of all Caucasians with blue eyes. In this haplotype, variations in rs1129038 and rs12913832 are relatively common in Caucasians though rare among other ethnic groups. The 'h-1' haplotype found in homozygous state in 97% of individuals with blue eye color is composed as follows : rs4778241(C) rs1129038(A) rs12593929(A) rs12913832(G) rs7183877(C) rs3935591(G) rs7170852(A) rs2238289(T) rs3940...
61.7	rs1881747 (T;T)	1.24x increased risk for LOAD

			Nominally significant association found for this SNP with late-onset Alzheimer's disease (odds ratio 1.24, p=0.011) in a study of ~1000 Caucasian patients, but it would not have withstood statistical correction for multiple testing.
61.7	rs13149290 (C;C)	somewhat higher risk for prostate cancer

			rs13149290 is one of seven SNPs found in a combined study of over 1,000 patients to be associated with increased risk for prostate cancer. The risk allele for this SNP is (C); and while the odds ratio was not specifically reported, the probability of false significance (not permuted though) was given as p=2.5 x 10e-5, using a dominant model of risk.
61.7	rs629242 (C;C)	normal risk

			rs629242 is one of seven SNPs found in a combined study of over 1,000 patients to be associated with increased risk for prostate cancer. The risk allele for this SNP is (T); and while the odds ratio was not specifically reported, the probability of false significance (not permuted though) was given as p=7.2 x 10e-7, using an additive model of risk.
62.7	rs6822844 (G;G)

			association with rheumatoid arthritis and type-1 diabetes point to a general risk locus for autoimmune diseases. Also, of SNPs outside the HLA region, this SNP and one other (rs13119723) in the region of the IL21 gene showed the strongest association with celiac disease in a study of ~800 Caucasian patients and a meta-analysis of two further populations.
62.7	rs9357271 (T;T)	common

			rs9357271, a SNP located in the BTBD9 gene region, has been linked to a lower frequency of restless legs syndrome, a common sleep disorder, with an overall odds ratio of 0.63 (CI: 0.52-0.75) for the (C) minor allele.
63.3	rs1954787 (C;T)	normal risk

			rs1954787, located in an intron of the HTR2A gene, was found to be associated with a somewhat increased rate of successful response to treatment of depression with the drug citalopram. From the abstract of this article: 'The effect size of (this) GRIK4 marker alone was modest, but homozygote carriers of the treatment-response-associated marker alleles of both the GRIK4 and HTR2A (see rs7997012) genes were 23% less likely to experience nonresponse to (citalopram) treatment relative to participants who did not carry any of these marker alleles.' * See also [http://www.anxietyinsights.info/antipressant_effectiveness_predicted_by_gene_variation.htm Anxiety Blog] posting
63.3	rs2302009 (T;T)	normal

			rs2302009 is a SNP located in the 3' untranslated region of the CCL26 gene. This gene (and this SNP) were discovered to be strongly associated with 117 patients with eosinophilic esophagitis, a form of esophagitis (or inflammation of the esophagus) that shares many symptoms with gastroesophageal reflux disease (GERD). rs2302009(G) is the risk allele. The rs2302009(G;G) homozygous genotype is the most predisposed to developing eosinophilic esophagitis (odds ratio 4.55, CI 1.7112.39). The heterozgyote (rs2302009(G;T)) genotype's risk was indistinguishable statistically from the normal rs23020099(T;T) genotype. [omim:ESOPHAGITIS, EOSINOPHILIC, SUSCEPTIBILITY TO]
63.3	rs6647 (T;T)

			[omim:PI M1-VAL213]
63.3	rs9296249 (T;T)	common

			rs9296249, a SNP located in the BTBD9 gene region, has been linked to a lower frequency of restless legs syndrome, a common sleep disorder, with an overall odds ratio of 0.62 (CI: 0.52-0.75) for the (C) minor allele.
63.3	rs34330 (C;C)	normal risk

			Category:interesting rs34330 shows an association with breast cancer in a British study involving ~2300 patients. The odds ratio for the (T;T) vs (C;C) homozygotes is 1.22 (CI: 1.02-1.47, p=0.013). found a significant association between rs34330 (-79C/T) and prostate cancer see also [http://www.genome.jp/dbget-bin/www_bget?omim+176807 omim 176807]
64.4	rs6718526 (C;C)	1.9x risk

			rs6718526 has been reported in a large study to be associated with type-2 diabetes. The risk allele (oriented to the dbSNP entry) is (C); the odds ratio associated with heterozygotes is 1.49 (CI 1.05-2.11), and for homozygotes, 1.86 (CI 1.32-2.63).
65.0	rs11030104 (A;A)

			Alzheimer's disease risk for non ApoE4 carriers is affected by the heterozygous form of rs6265, as well as the diplotypes of rs6265, rs11030104, and rs2049045.
65.0	rs11701 (T;T)

			The common form at this site in most populations is rs11701(T), and the variant form is rs11701(G). Having at least one copy of this variant form, rs11701(G), has been associated with an increased incidence of ALS in Scottish and Irish populations studied, but not in populations from the U.S., Sweden, or England. *rs11701 In Irish amyotrophic lateral sclerosis patients, there was a significant allelic association with the rs11701 SNP & a new mutation (K40I) that potentially inhibits angiogenin function.
66.7	rs2619522 (T;T)

			[http://originsgenomeresources.net/musings/?p=85 blog] In a population of healthy individuals, those that carry common variants (such as rs760761, rs1018381, rs2619522) located in the dysbindin (DTNBP1) gene, a risk factor for schizophrenia, show minor cognitive impairments such as decreased attentional capacity, worse performance on memory tasks, and alterations in schizotypal beliefs and experiences.
66.7	rs1801157 (G;G)

			rs1801157(A) was associated with protection against infection (OR=0.63, P=0.01). In the MACS cohort, rs1801157 was associated with AIDS-87 (RH=0.31, P=0.02) and with death (RH=0.18, P=0.02). HIV-1/AIDS
66.7	rs2144908 (G;G)

			1. effects type-2 diabetes 2. pmids15047633 15504983 15735892 16522129 16522130 16523192 16523193 16523194 16752173 popular in pubmed
66.7	rs1047972 (C;C)

			influences mitosis associated with cancer * breast cancer * colorectal cancer * gastric cancer
66.7	rs2032631 (A;A)
			[haplogroup:P]
			[haplogroup:?]
66.7	rs800292 (C;C)	normal

			rs800292 is a SNP in the complement factor H CFH gene; it has been linked to blindness in age related macular degeneration. This SNP is also known as 184G>A or Val62Ile. A haplotype of rs1061170 rs3753394 rs800292 rs1329428 (TGTC) was found to confer a significantly increased likelihood of exudative AMD CFH variations appear to contribute to ARMD in Caucasians, but not in Japanese A study of Chinese AMD patients reports that carriers of both rs11200638 and rs800292 risk alleles pushes the odds ratio for AMD up to 23x. Overall, an 'extremely high' population attributable risk (PAR) of 78% reported for these SNPs.
66.7	rs2518224 (A;A)	normal

			This SNP, located in an intron of the GRIK2 gene, has been linked in one study to increased thoughts of suicide in patients using the anti-depressant drug citalopram. The risk is only seen for individuals carrying two rs2518224(C) alleles, i.e. the rs2518224(C;C) homozygotes. The odds ratio for these individuals is 8.2. If the individual also has at least one rs4825476(G) allele, the odds ratio for having suicidal thoughts is increased to ~15x (CI: 3.7 - 60.6).
66.7	rs2238472 (G;G)

			[omim:PSEUDOXANTHOMA ELASTICUM]
66.7	rs1024611 (T;T)	normal risk

			rs1024611, also known as the -2578A>G SNP due to its position in the promoter of the monocyte chemoattractant protein-1 MCP-1 CCL2 gene, influences the production of its corresponding protein, a chemokine involved in inflammatory responses. In a study focusing on 679 apparently healthy siblings of people with premature heart disease, investigators found that carriers of an rs1024611(C) allele - oriented as in dbSNP, not as published - independently predicted the risk of exercise induced ischemia in general. The odds ratio was reported to be 1.86 (CI: 1.14-3.04, p=0.014), regardless of race, age, sex and other factors. However, it is not clear if this risk carries over to individuals who lack siblings with heart disease.
66.7	rs197414 (C;C)

			The homozygous was associated with a significantly increased bladder cancer risk [odds ratios (OR), 2.40; 95% confidence interval (95% CI), 1.04-5.56]
66.7	rs2267668 (A;A)

			rs1053049, rs6902123, and rs2267668 in PPARD affect Lifestyle Intervention induced changes in overall adiposity, hepatic fat storage, and relative muscle mass. Our findings provide a mechanistic explanation for the involvement of these genetic variations in the development of insulin resistance and type-2 diabetes.
67.2	rs4570625 (G;G)	higher scores on anxiety-related personality traits

			rs4570625 and rs4565946 linked to the pathogenesis of early-onset obsessive compulsive disorder rs4570625 and rs11178997 in TPH2's regulatory region display preferential transmission [http://originsgenomeresources.net/musings/?p=127 originsgenomeresources] Nerd snp
67.2	rs1800449 (G;G)

			[omim:LYSYL OXIDASE POLYMORPHISM]
67.8	rs760761 (C;C)

			[http://originsgenomeresources.net/musings/?p=85 blog] In a population of healthy individuals, those that carry common variants (such as rs760761, rs1018381, rs2619522) located in the dysbindin (DTNBP1) gene, a risk factor for schizophrenia, show minor cognitive impairments such as decreased attentional capacity, worse performance on memory tasks, and alterations in schizotypal beliefs and experiences.
67.8	rs1799884 (G;G)	normal

			rs1799884, known also as the -30 SNP of the GCK gene, has been associated with type-2 diabetes. This SNP is one of 4 relatively common SNPs reported to represent risk for type-2 diabetes in the DESIR prospective study of 3,877 Caucasian participants. Under a recessive model, the odds ratio for rs1799884(A;A) homozygotes is 2.70 (CI: 1.51-4.83, p=0.0008); under an additive model, the odds ratio is 1.34 (CI: 1.07-1.69, p=0.01). For the 4 SNPs, each risk allele increased type-2 diabetes risk by 1.34x (p=2x10e-6), with an odds ratio of 2.48 (CI: 1.59-3.86) for carriers of 4 or more compared to those with one or none (risk alleles).
68.3	rs6265 (G;G)	?

			This snp in BDNF seems to affect the risk of Alzheimer's disease. Alzheimer's disease risk for non ApoE4 carriers is affected by the heterozygous form of rs6265, as well as the diplotypes of rs6265, rs11030104, and rs2049045. The A allele may also be protective against depression when subjected to repeated defeat [http://originsgenomeresources.net/musings/?p=66 blog summary]
68.3	rs1805388 (C;C)

			[omim:MULTIPLE MYELOMA, RESISTANCE TO]
68.3	rs4458717 (T;T)

			Suspected of reproducibility problems based on [http://www.kk.org/quantifiedself/2008/05/testing-genetic-test-chips.php end user analysis] rs11149566 rs4458717 rs4660646 rs754499
68.3	rs2235067 (G;G)	7x more likely to respond to certain antidepressants

			rs2235067 is a SNP in the ABCB1 gene (also known as the MDR1 gene), which encodes a protein that transports certain molecules across the blood-brain barrier. SNPs in ABCB1 may thus influence the intracerebral concentrations of certain drugs and thus their efficacy or potential for adverse side effects. rs2235067 is one of 9 SNPs found within a tight linkage block (r² >= 0.8 ) such that the minor allele at any one of them predicts (with ~80%+ accuracy) that the other SNPs will also be the minor allele. The list of the 9 SNPs is shown below. When treated for depression with substrates of the protein encoded by ABCB1, carriers of one or two minor alleles at these ABCB1 SNPs have been reported to respond better than non-carriers. The antidepressant drugs that are known to be substra...
68.3	rs1799971 (A;A)

			The rs1799971(G) allele in exon 1 of the mu opiod receptor gene causes the normal amino acid at residue 40, asparagine, to be replaced by aspartic acid. Carriers of at least one rs1799971(G) allele appear to have stronger cravings for alcohol than carriers of two rs1799971(A) alleles, and are thus hypothesized to be more at higher risk for alcoholism. However, the research results are quite mixed, and there are other studies both agreeing or disagreeing with this finding [PMID 15525999, PMID 9399694, PMID 12960749]
68.3	rs12720067 (G;G)	7x more likely to respond to certain antidepressants

			rs12720067 is a SNP in the ABCB1 gene (also known as the MDR1 gene), which encodes a protein that transports certain molecules across the blood-brain barrier. SNPs in ABCB1 may thus influence the intracerebral concentrations of certain drugs and thus their efficacy or potential for adverse side effects. rs12720067 is one of 9 SNPs found within a tight linkage block (r² >= 0.8 ) such that the minor allele at any one of them predicts (with ~80%+ accuracy) that the other SNPs will also be the minor allele. The list of the 9 SNPs is shown below. When treated for depression with substrates of the protein encoded by ABCB1, carriers of one or two minor alleles at these ABCB1 SNPs have been reported to respond better than non-carriers. The antidepressant drugs that are known to be subst...
68.3	rs2235040 (G;G)	7x more likely to respond to certain antidepressants

			rs2235040 is a SNP in the ABCB1 gene (also known as the MDR1 gene), which encodes a protein that transports certain molecules across the blood-brain barrier. SNPs in ABCB1 may thus influence the intracerebral concentrations of certain drugs and thus their efficacy or potential for adverse side effects. rs2235040 is one of 9 SNPs found within a tight linkage block (r² >= 0.8 ) such that the minor allele at any one of them predicts (with ~80%+ accuracy) that the other SNPs will also be the minor allele. The list of the 9 SNPs is shown below. When treated for depression with substrates of the protein encoded by ABCB1, carriers of one or two minor alleles at these ABCB1 SNPs have been reported to respond better than non-carriers. The antidepressant drugs that are known to be substra...
68.3	rs2032583 (T;T)	7x less likely to respond to certain antidepressants

			rs2032583 is a SNP in the ABCB1 gene (also known as the MDR1 gene), which encodes a protein that transports certain molecules across the blood-brain barrier. SNPs in ABCB1 may thus influence the intracerebral concentrations of certain drugs and thus their efficacy or potential for adverse side effects. rs2032583 is one of 9 SNPs found within a tight linkage block (r² >= 0.8 ) such that the minor allele at any one of them predicts (with ~80%+ accuracy) that the other SNPs will also be the minor allele. The list of the 9 SNPs is shown below. When treated for depression with substrates of the protein encoded by ABCB1, carriers of one or two minor alleles at these ABCB1 SNPs have been reported to respond better than non-carriers. The antidepressant drugs that are known to be substra...
70.0	rs12203592 (C;C)

			[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.0040004 plos] rs12203592 showed the largest allele frequency difference between the Irish individuals and those individuals of Northern, Central European and Eastern European descent [http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000074 plos] associated with hair color rs12896399 rs12203592
70.0	rs17307070 (T;T)

			[haplogroup:?]
70.0	rs9786261 (A;A)
			[haplogroup:R]
			[haplogroup:?]
70.0	rs7892893 (C;C)

			[haplogroup:?]
70.0	rs2234922 (A;A)

			[omim:EPOXIDE HYDROLASE POLYMORPHISM]
70.0	rs2072493 (A;A)

			[omim:LEGIONNAIRE DISEASE, SUSCEPTIBILITY TO]
70.0	rs1801265 (T;T)

			[omim:DIHYDROPYRIMIDINE DEHYDROGENASE DEFICIENCY]
70.0	rs2836061 (C;C)

			This SNP was associated with amyotrophic lateral sclerosis (ALS) based on a study of 1,152 patients.
70.0	rs3948464 (C;C)

			associated with genetic susceptibility to tuberculosis in West Africa
70.0	rs4149056 (T;T)	normal

			rs4149056 is a SNP in the SLCO1B1 gene, which encodes the 'organic anion transporting polypeptide 1B1' (OATP1B1) protein. This protein, found primarily in the liver, regulates the uptake of numerous drugs and natural compounds. The rs4149056(C) allele gives rise to an amino acid change (from valine to alanine at residue 174) which has reduced uptake/transport activity. Therefore, drugs metabolized by OATP1B1 tend to build up to higher circulating concentrations than they would otherwise. Although there are also several other SNPs described from the SLCO1B1 gene, other than rs4149056, they don't (yet?) have obvious medical consequences . The drugs known (or in some cases, thought) to be metabolized less well by the variant OATP1B1 protein encoded by the rs4149056(C) allele include: *Several...
70.0	rs2230806 (G;G)

			[omim:CORONARY HEART DISEASE IN FAMILIAL HYPERCHOLESTEROLEMIA, PROTECTION AGAINST]
70.0	rs5918 (T;T)	average

			The 'A2' allele of the platelet specific alloantigen system is encoded by rs5918(C), and it has been implicated as increasing the risk of myocardial infarctions, heart disease, and resistance to blood-thinning benefits of aspirin. On it's own, the A2 allele is implicated especially in early onset heart disease ; in combination with the 4G allele of the PAI1 gene, rs1799889, the increased risk of myocardial infarction in a Finnish study population was 4 fold higher (odds ratio = 4.5, p=0.001), particularly in males (odds ratio = 6.4, p=0.0005) . A2 allele carriers also appear to be relatively resistant to the anti-thrombotic (i.e. anti-clotting) actions normally associated with aspirin use. A protective effect of rs5918 has also been observed for the development of Non-Hodgkin Lymphoma, bot...
70.0	rs1800450 (G;G)

			pulmonary morbidity in preterm infants. related to non-Hodgkin's lymphoma [omim:MANNOSE-BINDING PROTEIN DEFICIENCY]
70.0	rs17315772 (A;A)

			[haplogroup:?]
70.0	rs17250121 (T;T)
			[haplogroup:K-R]
			[haplogroup:?]
70.0	rs9785740 (G;G)
			[haplogroup:P]
			[haplogroup:?]
70.0	rs3853054 (A;A)

			[haplogroup:?]
71.2	rs6439886 (A;A)	normal form

			Associated with episodic memory performance
71.2	rs3756450 (T;T)

			schizophrenia p = 0.035
71.7	rs1566734 (T;T)

			[omim:COLON CANCER, SOMATIC]
71.7	rs2230808 (G;G)

			rs2297404, rs2230808, and rs2020927 haplotype (CAC) was more prevalent in the Alzheimer's disease group (0.323 in AD vs. 0.202 in control); while haplotype1 (TGG) was over-represented in the healthy controls (0.595 in control vs. 0.493 in AD)
71.7	rs4779584 (C;C)	average

			A study of 7000+ UK patients with colorectal cancer identified two SNPs that increase disease risk, one of which is rs4779584. Inheriting the rs4779584(T) risk allele is estimated to increase overall risk odds by 1.26x (CI: 1.19-1.34, p=4x10e-14). When analyzing data between genotypes, the odds ratios reported for heterozygotes was 1.23x (CI:1.13-1.33), and for rs4779584(T;T) homozygotes, 1.70 (CI: 1.41-2.04). Inheriting the risk variant at both SNP loci (i.e. rs4779584 and rs6983267) is estimated to increase the overall risk of developing colorectal cancer about 3 fold. The authors of this study are quoted as saying that 'the lifetime risk [of bowel cancer] is about 5% in the UK so it's going up to 7% or so if you've got both bad copies of a variant.' [http://www.nature.com/ng/journal/vao...
71.7	rs2267013 (A;A)	normal risk

			rs2267013, a SNP in the BCR gene on chromosome 22, has been associated with increased risk for depression. The odds ratio for carriers of the minor allele (G) are reported as 1.27 (p=0.044) based on a study of 329 Japanese patients.
71.7	rs13119723 (A;A)

			Of SNPs outside the HLA region, this SNP and one other (rs6822844) in the region of the IL21 gene showed the strongest association with celiac disease in a study of ~800 Caucasian patients and a meta-analysis of two further populations.
71.7	rs6339 (G;G)

			[omim:THYROID CARCINOMA, FAMILIAL MEDULLARY]
71.7	rs2071421 (A;A)

			[omim:ARYLSULFATASE A POLYMORPHISM]
71.7	rs2070874 (C;C)

			Visceral leishmaniasis (VL) caused by Leishmania chagasi is endemic to northeast Brazil. A positive delayed-type hypersensitivity skin test response (DTH+) is a marker for acquired resistance to disease. the DTH- phenotype was associated with SNP rs2070874 at IL4 (OR 3.14; P=0.006; 95% CI=1.38-7.14), and SNP rs30740 between LECT2 and TGFBI (OR 3.00; P=0.042; 95% CI=1.04-8.65)
71.7	rs1800169 (G;G)	greater relative benefit of iloperidone to schizophrenics

			rs1800169 is a SNP in the ciliary neurotrophic factor CNTF gene. In a study of 417 patients with schizophrenia, 279 were treated with iloperidone while 138 were treated with placebo. Iloperidone significantly improved in 6 clinical scores versus placebo. rs1800169(G;G) homozygotes showed greater improvement with iloperidone compared to placebo for 3 of the clinical scores compared to carriers of a rs1800169(A) allele.
72.9	rs17234657 (T;T)	normal

			rs17234657 has been reported in a large study to be associated with Crohn's disease. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.54 (CI 1.34-1.76), and for homozygotes, 2.32 (CI 1.59-3.39).
73.3	rs10498091 (G;G)

			Left ventricle mass, rs10498091 (p = 5.68*10(-6));
73.3	rs4968451 (A;A)	normal

			rs4968451, which is in a breast cancer susceptibility gene, was associated with increased risk of meningioma, a common form of brain tumor, in a combination of five studies totaling 631 European patients. The odds ratio was 1.57 (CI: 1.28-1.93, p=.009 after adjusting for multiple testing) for the risk allele, rs4988451(C). Around 30% of Europeans carry one of risk genotypes, i.e. rs4968451(A;C) or (C;C); and perhaps 16% of meningiomas might be associated with this SNP.
73.3	rs1057141 (A;A)

			[omim:PEPTIDE TRANSPORTER PSF1 POLYMORPHISM]
73.3	rs1676486 (G;G)	average

			Lumbar disc herniation (LDH), a form of lumbar disc disease, is one of the most common musculoskeletal diseases. rs1676486, a SNP also known as c.4603C-->T in the COLL11A1 gene (one of 3 Type XI collagen genes), has been implicated in a study of ~800 Japanese patients as being associated with LDH. The risk allele in dbSNP orientation is (A), and the odds ratio associated with the allele is 1.42 (CI: 1.23 - 1.65).
74.1	rs1805007 (C;C)	normal risk

			rs1805007, known as Arg151Cys or R151C, one of several SNPs in the MC1R gene associated with red hair (redheads), and in redheaded females, linked to being more responsive to the anesthetics pentazocine, nalbuphine, and butorphanol, often used by dentists [PMID 9571181, PMID 12663858, PMID 18488028] The risk allele is rs1805007(T), compared with the wild-type rs1805007(C) allele. The risk allele has also been reported in several studies to be associated with increased risk for melanoma. For example, an odds ratio of 2.94 (CI: 1.04-8.31) has been reported for an Italian population , and similarly an odds ratio of 2.9 has been reported for a Polish population . [http://yannklimentidis.blogspot.com/2008/02/mc1r-genotypes-skin-cancer-risk-and.html blog] about designing melanocortin analogs spe...
74.6	rs906807 (G;G)

			[omim:PARKINSON DISEASE, SUSCEPTIBILITY TO]
75.0	rs5400 (C;C)

			rs5400(T;T) carriers had a significantly higher intake of sugars [http://skeptalchemist.blogspot.com/2008/05/finally-excuse-for-my-sweet-tooth.html blog] discussion
75.0	rs10272438 (A;A)

			analysis of a published data set on age related macular degeneration revealed an unreported haplotype near rs10272438 (P value = 0.0024).
75.0	rs1801725 (G;G)

			[omim:CALCIUM, SERUM LEVELS OF]
75.0	rs1800454 (G;G)	normal

			[omim:PEPTIDE TRANSPORTER PSF2 POLYMORPHISM]
76.7	rs2302765 (A;A)

			Variations in this snp have been linked to nicotine dependence [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16874522&query_hl=3&itool=pubmed_docsum]
76.7	rs2302763 (T;T)

			Variations in this snp have been linked to nicotine dependence
76.7	rs288326 (G;G)

			[omim:OSTEOARTHRITIS OF HIP, FEMALE-SPECIFIC, SUSCEPTIBILITY TO]
76.7	rs7723605 (T;T)

			Originally reported to be one of 13 SNPs found in whole genome association study to be associated with Parkinson's disease. However, neither it (nor the other 13) appeared to be associated with Parkinson's disease in an independent study of 663 Caucasian patients.
76.7	rs1044498 (A;A)

			[http://yannklimentidis.blogspot.com/2008/02/snps-that-may-have-made-human.html blog] ENPP1 harbors a mutation with a derived state known to protect against obesity and type II diabetes27 that is present in 90% of non-Africans but virtually absent in Africans [omim:INSULIN RESISTANCE, SUSCEPTIBILITY TO]
76.7	rs1156044 (T;T)

			rs1156044(A) was significantly associated with bipolar disorder (p = 0.013) but differed in allele (rs1156044 G allele) from that previously reported as associated with BD.
76.7	rs4399848 (G;G)	Homozygous major

			SNP rs4399848 (Chr 3 at 28.679467 Mb, band 3p24.1, dbSNP build 128) is associated weakly with hypertension in a genome-wide association study by the Wellcome Trust Case Control Consortium published in Nature (2007, appendix Table 7, page 40) . The so-called single point P is less than 0.0004 (4.44E-04). This statistic is relatively uninformative without follow-up study and a larger sample size. The (G;G) genotype is ancestral and has a frequency close to 100% in the Yourba population (Ibadan, Nigeria) and approximately 96-98% in Han Chinese. The (A;G) heterozygote has a frequency of up to about 25% in some European populations (Perlegen and HapMap). The (A;A) minor genotype is rare. The presumed effects of the A allele on risk of hypertension are likely to be very low and are still controv...
77.6	rs1076560 (C;C)

			rs1076560 is located in intron 6 of the dopamine receptor D2 gene. In one study of Japanese males, rs1076560(A) alleles were 1.3 fold more associated with Alcoholism than the rs1076560(C) alleles. The DRD2 risk allele A was more prevalent in the alcoholic patients than in the healthy controls. These data identify rs1076560 as a potentially important variable in the development of alcoholism.
78.0	rs3736228 (C;C)	normal

			rs3736228 is a SNP in the LRP5 gene that is also known as Ala1330Val; the more common (C) allele encodes the Ala (alanine), while the rarer (T) allele encodes the Val (valine), which is the risk allele. rs3736228(T) is associated with vertebral fractures and reduced bone mineral density (BMD), with an overall odds ratio for fractures of 1.06 per allele (CI: 1.01-1.12; 7802 fractures among 31,199 individuals studied). More specifically, the rs3736228(T) allele was associated with reduced lumbar spine BMD (p = 2.6 x 10^-9), and femoral neck BMD (p = 5.0 x 10^-6). Note that rs4988321, another LRP5 SNP (also known as Val667Met), was independently associated with BMD in this same study. [http://www.medpagetoday.com/Endocrinology/Osteoporosis/tb/9271 news] rs3736228 was assoc...
78.0	rs2066844 (C;C)

			rs2066844 is mentioned in as being strongly associated with Crohn's disease [omim:CROHN DISEASE, SUSCEPTIBILITY TO]
78.0	rs7495174 (A;A)	blue/gray eyes more likely

			rs7495174 is located in intron 1 of the OCA2 gene. The (A) allele (in dbSNP orientation) is associated with blue or green eye color in Caucasians. . This SNP is 1 of 3 SNPs defining a haplotype that has been studied for association with eye color. The full details on the correspondence between the haplotype and eye color can be found on the OCA2 page.
78.3	rs7530511 (C;C)	normal

			IL23R gene SNP, part of a haplotype with rs11209026 associated with psoriasis. In a study of 216 North American patients with Graves' disease, the homozygous rs10889677(T;T) genotype was significantly associated with Graves' disease but not specifically with Graves ophthalmopathy; the odds ratio was 9.4 (p=0.02).
78.3	rs9300039 (C;C)	>1.5x risk for T2D

			rs9300039, a SNP on chromosome 11 that is unusual is being over 1,000,000 base-pairs away from the nearest known gene, has been identified as a risk factor for type-2 diabetes in a study of over 2,000 Caucasian patients. The odds ratio for the risk allele (rs9300039(C)) was 1.48, (CI: 1.28-1.71, p=5.7x10e-8). This SNP is also mentioned in a related [http://suicyte.wordpress.com/2007/05/28/soul-searching-ii/ blog] series.
78.3	rs6503691 (C;C)

			breast cancer rs6503691 rs7211777 Carriers of the AC haplotype, which represents the variant alleles of both SNPs, were at an increased risk (OR = 1.41, 95% CI 1.09-1.82). A decreased risk was observed for carriers of the AT haplotype (OR = 0.60, 95% CI 0.38-0.94). Furthermore, individuals with the AC/GC diplotype were at a significantly increased risk (OR = 1.88, 95% CI 1.13-3.14)
78.3	rs3129763 (G;G)

			Source [http://www.nature.com/ng/journal/v38/n10/fig_tab/ng1885_T1.html nature] Graves' disease or myasthenia gravis rs3129763(C) + rs4639334(C)
78.8	rs4553808 (A;A)	normal

			rs4553808, also known as A/G-1661, is a SNP in the upstream activator sequence of the cytotoxic T lymphocyte associated antigen-4 CTLA4 gene. This gene encodes the CD152 antigen. A study of 165 Swedish myasthenia gravis patients concluded that the rs4553808(G;G) homozygotes had an odds ratio of 0.05 (CI: 0.00286-0.874, p=0.0023) for the disease compared to healthy individuals, while the rs4553808(G) allele showed a less dramatic reduction in risk, with an odds ratio of 0.578 (CI: 0.373-0.897, p=0.015).
79.2	rs1799853 (C;C)	Arg:Arg; no change in warfarin metabolism

			rs1799853 is a SNP in the CYP2C9 gene. The rs1799853(T) allele encodes a variant amino acid, cysteine, which has been linked to poor metabolism of warfarin and thus sensitivity . The common nomenclature for this polymorphism is CYP2C92 (Cys amino acid, T allele). The effect of CYP2C9 variants on drug metabolism cannot be predicted without considering CYP2C92, defined as the common loss of function variant [rs1799853(T)] [http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=1799853] (NM_000771:c.430C>T, NP_000762:p.144R>C) [http://www.pharmgkb.org/search/annotatedGene/cyp2c9/].
79.7	rs6442925 (C;C)

			Along with rs534654 and rs1534891, this SNP, rs6442925, is part of a 3-SNP (multi-locus) interaction that is associated with bipolar disorder.
79.7	rs2200733 (C;C)	1.4x increased risk of atrial fibrillation

			Two SNPs from chromosome 4q25, rs2200733 and rs10033464, were found to be associated with atrial fibrillation in a study of both European and Asian populations. The odds ratio associated with one or more copies of either risk allele was ~1.4x.
80.0	rs10033464 (G;G)	1.4x increased risk of atrial fibrillation

			Two SNPs from chromosome 4q25, rs2200733 and rs10033464, were found to be associated with atrial fibrillation in a study of both European and Asian populations. The odds ratio associated with one or more copies of either risk allele was ~1.4x.
80.0	rs1805005 (G;G)

			rs1805005, known as Val60Leu or V60L, is a SNP in the MC1R gene associated with light blond hair in one study. The risk allele is rs1805005(T), compared with the wild-type rs1805005(G) allele. See also [http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=155555&a=155555_AllelicVariant0006 OMIM 155555.0006]
80.0	rs3026785 (T;T)

			associated with protection from Hirschsprung disease see omim [http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=164761 164761]
80.0	rs6267 (G;G)

			[omim:SCHIZOPHRENIA, SUSCEPTIBILITY TO]
80.0	rs4648317 (C;C)	normal

			rs4648317, a SNP in the dopamine D2 receptor DRD2 gene, has been linked to higher rates of smoking and higher nicotine dependence scores, based on a study of ~220 adolescents. The risk allele rs4648317(T).
80.0	rs683395 (T;T)	normal

			rs683395 has been reported in a large study to be associated with bipolar disorder. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.47 (CI 1.26-1.71), and for homozygotes, 1.3 (CI 0.69-2.46).
80.0	rs2073838 (G;G)

			rs2073838, a SNP in the SLC22A4 gene, has been associated along with rs3792876 (another SNP in the SLC22A4 gene) with an autoimmune disease, in this case, rheumatoid arthritis, odds ratio = 1.98 (CI = 1.432.75), from 830 cases and 658 controls. The risk allele for rs2073838 appears to be (A).
80.0	rs2811712 (A;A)	normal risk

			rs2811712 is a SNP associated with physical function in older individuals, and thus indirectly associated with longevity. In a study ultimately totaling over 3,300 elderly Caucasian individuals, the less common rs2811712(G) allele was associated with reduced physical impairment. Overall, severely limited physical function was present in 15.0% of the more common rs2811712(A;A) homozygotes, versus 7.0% of the rs2811712(G;G) homozygotes, yielding a per risk allele odds ratio of 1.48 (CI: 1.17-1.88, p=0.001).
81.4	rs1534891 (C;C)

			Along with rs6442925 and rs534654, this SNP, rs1534891, is part of a 3-SNP (multi-locus) interaction that is associated with bipolar disorder.
81.7	rs1355920 (A;A)

			associated with specific patterns of brain activity. rs3087454 rs1355920 rs7520974 rs885834
81.7	rs2040410 (G;G)

			Source [http://www.nature.com/ng/journal/v38/n10/fig_tab/ng1885_T1.html nature] Type 1 diabetes or SLE rs2040410
81.7	rs3770748 (T;T)	average risk?

			rs3770748, a SNP in an intron of the QPCT gene, was studied in a population of ~200 Chinese osteoporosis patients. Heterozygotes appeared to be at higher risk than either homozygote, and the association was statistically strongest in post-menopausal women.
81.7	rs1800458 (G;G)

			[omim:TRANSTHYRETIN SER-6 POLYMORPHISM]
81.7	rs6136 (A;A)

			cardiovascular risk
81.7	rs2837960 (T;T)	normal

			rs2837960 has been reported in a large study to be associated with rheumatoid arthritis. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 0.95 (CI 0.83-1.08), and for homozygotes, 2.30 (CI 1.64-3.23).
81.7	rs2187668 (G;G)	average

			In at least UK populations, and perhaps others, SNP rs2187668 is a tag SNP for the HLA-DRB10301 allele. The HLA-DRB10301 allele is the allele presenting the highest risk for developing lupus, and it appears to act in a dominant manner (i.e. inheriting 2 copies is no worse than inheriting 1 copy). In dbSNP orientation, the risk allele is rs2187668(A), with an odds ratio of 2.3x (CI: 1.7 - 3.2, permuted p < 0.0001). From individuals with the most common rs2187668](G;G) genotype, risk is reduced for celiac disease, with an odds ratio of 0.30x according to a study of ~800 patients.
83.3	rs3132453 (C;C)

			rs3132453, a SNP in the BAT2 gene also known as V1883L, is associated with reduced risk for developing Non-Hodgkin Lymphoma based on a study of 458 patients. The odds ratio is 0.64 (CI: 0.45-0.90, p<0.01).
83.3	rs12951053 (A;A)

			rs17887200 and rs12951053 associated with ER negative breast cancer tumors (1.48 (1.11-1.93) p-trend = 0.01 and 1.29 (1.06-1.58) p-trend = 0.009, respectively)
83.3	rs8111071 (A;A)	normal

			rs8111071 has been reported in a large study to be associated with Crohn's disease. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.47 (CI 1.25-1.73), and for homozygotes, 1.28 (CI 0.56-2.88).
83.3	rs4639334 (G;G)

			Source [http://www.nature.com/ng/journal/v38/n10/fig_tab/ng1885_T1.html nature] Graves' disease or myasthenia gravis rs3129763(C) + rs4639334(C)
83.3	rs2279420 (T;T)	0.79x decreased risk for LOAD

			Nominally significant association found for this SNP with late-onset Alzheimer's disease (odds ratio 0.79, p=0.022) in a study of ~1000 Caucasian patients, but it would not have withstood statistical correction for multiple testing.
83.3	rs2303064 (G;G)

			rs2303064, a SNP in the SPINK5 gene, has been associated with susceptibility to atopic dermatitis.
83.3	rs1446109 (A;A)

			having minor alleles at all 3 of rs1446109-rs1007371-rs723524 may affect left-right asymmetrical brain function, such as handedness, and much of human cognition, behavior and emotion. [https://genepi.qimr.edu.au/contents/p/staff/CV522.pdf pdf full paper]
83.3	rs5361 (A;A)	normal risk

			The rs5361 Ser128Arg variation in this gene, known as E-selectin, is linked to several thrombotic disorders. rs5361(C;C) homozygous carriers of the Ser128Arg allele are at a 4X higher risk for recurrent venous thromboembolism (VTE); heterozygous carriers are not at increased risk. .
83.3	rs3218536 (G;G)	normal risk

			rs3218536, a relatively rare SNP also known as Arg188His located in the DNA-repair gene XRCC2, is associated with a lowered risk for breast cancer based on a study of 1,100 Cypriot women. The odds ratio for the His-encoding rs3218536(A) allele carriers is homozygote is 0.79, CI: 0.62-1.00, p=0.05. rs3218536(A) carriers also appear to be at lower risk for epithelial ovarian cancer. In a study of ~1,600 cases, the odds ratio for rs3218536(A;G) heterozygotes was 0.8 (CI: 0.7-1.0) and for the (quite rare) rs3218536(A;A) homozygotes 0.3 (0.1-0.9).
84.7	rs9289231 (T;T)

			In a study of early onset coronary artery disease, rs9289231, the risk allele of this SNP, located in the kalirin KALRN gene, was associated with increased odds (OR 2.1), and also for increased atherosclerosis burden.
85.0	rs6314 (C;C)	higher risk for RA

			rs6314 is part of a 4-SNP haplotype in the serotonin 2A receptor gene HTR2A that has been associated with rheumatoid arthritis in a study of 1800 European patients. The risk allele is rs6314(C). The overall risk for the haplotype CTCC of SNPs rs6311-rs1328674-rs6313-rs6314 is 1.68 (CI: 1.20 - 2.34, p = 0.02). Note: the orientation of rs1328674 in dbSNP is opposite that cited by this publication; therefore, with respect to dbSNP, the haplotype of risk as cited above is CACC rather than CTCC.
85.0	rs3750861 (C;C)

			rs10508266 and rs3750861 shows significant association with lung cancer risk rs3750861 affects expression of KLF6 splicing variants in prostate cancer and we found that its rare allele is associated with reduced lung cancer risk
85.0	rs1805018 (T;T)

			asthma related [omim:ASTHMA AND ATOPY, SUSCEPTIBILITY TO]
85.0	rs450046 (T;T)

			[omim:HYPERPROLINEMIA, TYPE I]
86.4	rs2273206 (G;G)

			haplotype less common in schizophrenia rs2273206(T), rs2273207(G), rs2228480(G).
86.7	rs6802898 (C;C)

			associated with type-2 diabetes
86.7	rs696217 (G;G)


86.7	rs11465804 (T;T)	normal risk

			rs11465804 is one of several SNPs in the IL23R gene that has been shown in a large (over 1,000 Caucasian patients) study to be associated with ankylosing spondylitis. The odds ratio is 0.68 (p=0.0002).[PMID 17952073, PMID 18037607]
86.7	rs1799999 (G;G)	normal risk

			[omim:INSULIN RESISTANCE, SUSCEPTIBILITY TO]
88.1	rs11209026 (G;G)	common

			A relatively rare allele at SNP rs11209026, in the IL23R gene, appears to provide a fairly strong protective effect against the development of Crohn's disease in both Jewish and non-Jewish populations. Note that in this study the (A;A) and (A;G) genotypes were combined for statistical reasons (there were too few (A;A) individuals to study by themselves), so the risk is shown as equal for both. associated With Inflammatory Bowel Diseases but Not With Celiac Disease rs11209026 had a protective effect for IBD in the case-control analysis (odds ratio [OR] 0.19, 95% confidence interval [CI] 0.10-0.37, P= 6.6E-09). Both CD (OR 0.14, CI 0.06-0.37, P= 3.9E-07) and UC (OR 0.33, CI 0.15-0.73, P= 1.4E-03) were associated with IL23R. rs2241880 was associated with CD susceptibility (OR 1.36, CI 1.12-...
88.1	rs8028689 (T;T)	blue eye color if part of blue eye color haplotype

			rs8028689 is part of a haplotype spanning 166kB on chromosome 15, defined by 13 SNPs listed below, found in 97% of all Caucasians with blue eyes. In this haplotype, variations in rs1129038 and rs12913832 are relatively common in Caucasians though rare among other ethnic groups. The 'h-1' haplotype found in homozygous state in 97% of individuals with blue eye color is composed as follows : rs4778241(C) rs1129038(A) rs12593929(A) rs12913832(G) rs7183877(C) rs3935591(G) rs7170852(A) rs2238289(T) rs3940272(C) rs8028689(T) rs2240203(A) rs11631797(G) rs916977(G)
88.1	rs9494266 (G;G)

			Originally reported to be associated with type-2 diabetes in a genome-wide association study; yet then reported not to be associated with either T2D or related metabolic traits in a large Danish population (ultimately 17,000 patients for the latter study).
88.3	rs1528133 (A;A)	normal risk

			rs1528133, a SNP in the TUB gene, was found in a study of 492 unrelated type-2 diabetes patients to have a significant effect on body mass index and thus obesity (1.54 kg/m(2), p= 0.006). When two populations were combined, totaling ~1200 patients, the risk allele (rs1528133(C) averaged an increase of 0.54 kg/m2 (CI: 0.19-1.26). Two additional TUB SNPs, rs2272382, and rs2272383, mapping to the 3' end of the gene showed similar associations and were in linkage disequilibrium with rs1528133. A follow-up study of 1,680 middle-aged Dutch women found that this allele, rs1528133(C), was significantly associated with increased weight (+1.88 kg, p=0.022) and body mass index (+0.56 units, p= 0.05). rs1528133(C) carriers were also associated with an increased glycemic load of 1.85 units compared wi...
88.3	rs16139 (A;A)

			[omim:NEUROPEPTIDE Y POLYMORPHISM]
88.3	rs1057910 (A;A)	Ile:Ile; no effect on warfarin metabolism

			SNP rs1057910(A), located in the cytochrome p450 CYP2C9 gene, most commonly encodes the amino acid isoleucine at position 359, and the resulting allele is also known as CYP2C91. rs1057910(C) encodes a leucine at this same position, and the resulting allele is called CYP2C93. The effect of CYP2C9 variants on drug metabolism cannot be predicted without considering CYP2C92, defined as the common loss of function variant rs1799853(T) (NM_000771:c.430C>T, NP_000762:p.144R>C) [http://www.pharmgkb.org/search/annotatedGene/cyp2c9/]. Studies of the effects of these alleles include: rs1057910(C;C) genotypes may clear drugs like celecoxib (trade name Celebrex) twice as slowly as rs1057910(A;A) genotypes; the rs1057910(A;C) genotypes are in-between clearance rates. Lower clearance rates will lea...
89.7	rs2197423 (C;C)

			associated with type-2 diabetes
89.8	rs11162922 (A;A)	2x risk

			rs11162922 has been reported in a large study to be associated with rheumatoid arthritis. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.27 (CI 0.41-4.01), and for homozygotes, 2.00 (CI 0.64-6.20).
90.0	rs3804505 (C;C)	common

			[omim:MYOCLONIC EPILEPSY, JUVENILE, 1]
90.0	rs1535435 (G;G)

			Originally reported to be associated with type-2 diabetes in a genome-wide association study; yet then reported not to be associated with either T2D or related metabolic traits in a large Danish population (ultimately 17,000 patients for the latter study).
90.0	rs733618 (A;A)	normal

			rs733618, also known as T/C-1772, is a SNP in the upstream activator sequence of the cytotoxic T lymphocyte associated antigen-4 CTLA4 gene. This gene encodes the CD152 antigen. A study of 165 Swedish myasthenia gravis patients concluded that the rs733618(A;G) heterozygotes had an odds ratio of 1.87 (CI: 1.01-3.49, p=0.049) for the disease compared to healthy individuals, yet neither allele on its own showed increased risk. rs231775 (CTLA4_+49_G/A P=0.0219) and rs733618 (CTLA4_-1722_T/C P=0.0096) susceptibility to Graves' disease
90.0	rs1041981 (C;C)

			[omim:MYOCARDIAL INFARCTION, SUSCEPTIBILITY TO]
90.0	rs1328674 (G;G)	average

			rs1328675 is part of a 4-SNP haplotype in the serotonin 2A receptor gene HTR2A that has been associated with rheumatoid arthritis in a study of 1800 European patients. The risk allele is rs1328674(A) in dbSNP orientation. The overall risk for the haplotype CTCC of SNPs rs6311-rs1328674-rs6313-rs6314 is 1.68 (CI: 1.20 - 2.34, p = 0.02). This is actually quite close to the odds ratio calculated for rs1328674 by itself; OR of 1.62 (p = 0.007). Note: the orientation of rs1328674 in dbSNP is opposite that cited by this publication; therefore, with respect to dbSNP, the haplotype of risk as cited above should be CACC, rather than CTCC as published.
90.0	rs1800058 (C;C)

			This SNP, a variant in the ATM gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (T).
90.0	rs6336 (C;C)

			[omim:THYROID CARCINOMA, FAMILIAL MEDULLARY]
90.0	rs7183877 (C;C)	blue eye color if part of blue eye color haplotype

			rs7183877 is part of a haplotype spanning 166kB on chromosome 15, defined by 13 SNPs listed below, found in 97% of all Caucasians with blue eyes. In this haplotype, variations in rs1129038 and rs12913832 are relatively common in Caucasians though rare among other ethnic groups. The 'h-1' haplotype found in homozygous state in 97% of individuals with blue eye color is composed as follows : rs4778241(C) rs1129038(A) rs12593929(A) rs12913832(G) rs7183877(C) rs3935591(G) rs7170852(A) rs2238289(T) rs3940272(C) rs8028689(T) rs2240203(A) rs11631797(G) rs916977(G)
90.4	rs4986852 (G;G)

			[omim:BREAST-OVARIAN CANCER]
91.5	rs997509 (C;C)

			rs997509 increases the risk of Type-2 diabetes for the obese. *rs997509 we found a new SNP, rs997509, in intron 1 that is strongly associated with risk of type 2 diabetes in obese individuals.
91.5	rs16964201 (C;C)

			The research paper suggests that the 3 snps rs17703883, rs12594287 and rs16964201 affect bone mineral density in men.
91.5	rs2070075 (C;C)

			[omim:LOS ANGELES VARIANT]
91.7	rs1799950 (A;A)	normal breast cancer risk

			This SNP, a variant in the BRCA1 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. This particular SNP, rs1799950, was actually the only SNP of the 25 to have an increased odds ratio for breast cancer to be over 1.5 in carriers and to also be present at a minor allele frequency of over 5%. The odds ratio calculated was 1.72 (P = 0.0002). The risk (minor) allele is (G).
91.7	rs2066992 (G;G)

			rs2066992 coronary artery disease 190 affected Asian Indian sibling pairs
91.7	rs1800562 (G;G)	Normal/Common

			rs1800562 represents a SNP that accounts for ~85% of all cases of hemochromatosis, a disorder who's symptoms include cirrhosis of the liver, diabetes, hypermelanotic pigmentation of the skin, and heart failure. [http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=235200 OMIM] indicates that liver cancer is responsible for about one-third of deaths of rs1800562(A;A) homozygotes, and since hemochromatosis is a relatively easily treated disorder if diagnosed, this is a form of preventable cancer. The rs1800562(A) allele is known as the C282Y mutation, and it is found at a frequency of around 5-10% in many Caucasian populations, leading to an incidence of (A;A) homozygotes around 1 in 200. Early identification of rs1800562(A;A) homozygotes can prevent complications of hemochromatosis; however, ...
93.2	rs7965399 (T;T)

			linked to Prostate cancer
93.3	rs1799899 (G;G)

			it was concluded that PAI-1 promoter polymorphism 4G -> 5G (rs1799899) is not associated with the aggressiveness of disease in prostate cancer [omim:IRON DEFICIENCY ANEMIA, SUSCEPTIBILITY TO]
93.3	rs4769874 (G;G)

			rs4769874, also known as SG13S89, is an ALOX5AP gene SNP that has been defined as part of a haplotype potentially associated with risk for myocardial infarction or ischemic stroke. Details of this haplotype and several related studies are on the ALOX5AP page.
93.3	rs8176058 (C;C)

			[omim:KELL K/k BLOOD GROUP POLYMORPHISM]
93.3	rs4986790 (A;A)

			rs4986790, a SNP also known as Asp299Gly in the TLR4 gene, is often studied along with a cosegregating SNP known as Thr399Ile, rs4986791. (TLR4 encodes a receptor involved in the innate immune response.) Together, these SNPs have been reported to be associated with a wide variety of both infectious and non-infectious diseases, although there are conflicting or even contradictory results also reported in some cases. The risk allele for rs4986790 is (G). Reported associations include : * Diabetic neuropathy ** These SNPs may be protective * Heart disease Men with the risk alleles for both SNPs are at increased risk for myocardial infarction in this study of over 2000 individuals. rs4986790(G) carriers are not at increased risk for myocardial infartions, at least in this study of ~200...
93.3	rs4986791 (C;C)

			rs4986791, a SNP also known as Thr399Ile in the TLR4 gene, is often studied along with a cosegregating SNP known as Asp299Gly, rs4986790. (TLR4 encodes a receptor involved in the innate immune response.) Together, these SNPs have been reported to be associated with a wide variety of both infectious and non-infectious diseases, although there are conflicting or even contradictory results also reported in some cases. The risk allele for rs4986791 is (T). Reported associations include : * Diabetic neuropathy ** These SNPs may be protective * Heart disease Men with the risk alleles for both SNPs are at increased risk for myocardial infarction in this study of over 2000 individuals. rs4986790(G) carriers are not at increased risk for myocardial infartions, at least in this study of ~200...
94.7	rs820878 (C;C)

			[omim:SANDHOFF DISEASE, INFANTILE TYPE]
94.9	rs3807153 (T;T)	normal

			[omim:RENAL TUBULAR ACIDOSIS, DISTAL, AUTOSOMAL RECESSIVE]
94.9	rs10505483 (G;G)

			Associated with prostate cancer [http://www.biomedcentral.com/1471-2350/8/S1/S6/table/T4 table]
95.0	rs1801270 (C;C)	increased risk for lung cancer

			rs1801270 is a SNP known as p21 codon 31, although the gene now known to code for the p21 protein is termed CDKN1A, and has also been known as WAF1 and CIP1. Along with p53 codon 72 (rs1042522), it is one of the best studied SNPs due to its role in increased tumor susceptibility (and thus cancer). A study of ~150 lung cancer patients in Sweden found that the rs1801279(A) allele, encoding the amino acid Arg at codon 31, represented the risk allele (odds ratio 1.7, CI: 1.0-2.9), compared to healthy individuals. The difference was even more striking when compared to patients with chronic obstructive pulmonary disease (COPD), in which case the odds ratio was over 5. [omim:CIP1/WAF1 TUMOR-ASSOCIATED POLYMORPHISM 1]
95.0	rs1800056 (T;T)

			This SNP, a variant in the ATM gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (C).
95.0	rs1805389 (C;C)

			[omim:MULTIPLE MYELOMA, RESISTANCE TO]
95.0	rs1142345 (A;A)

			rs1142345 is a SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP is rs1142345(G), and it encodes the TPMT*3C allele. While still rare, it is more common in African-Americans (2.4% of all alleles) than in Caucasians.
95.0	rs1426654 (A;A)	probably light-skinned, European ancestry

			This SNP influences skin pigmentation. The allele p.A111T, rs1426654(A), indicates light-skinned european ancestry. [PMID 16847698, PMID 16357253] It appears as if this SNP is a relatively new one in human evolution; one estimate is that the rs1426654(A) allele, in other words, light skin pigmentation, spread through the European population around 6,000 - 12,000 years ago. Prior to that, 'European ancestors' were most likely relatively brown-skinned.
95.0	rs4988321 (G;G)	normal

			rs4988321 is a SNP in the LRP5 gene that is also known as Val667Met; the more common (G) allele encodes the Val (valine), while the rarer (A) allele encodes the Met (methionine), which is the risk allele. rs4988321(A) is associated with vertebral fractures and reduced bone mineral density (BMD), with an overall odds ratio for vertebral fractures of 1.26 per allele (CI: 1.08-1.47; 2001 fractures among 20,488 individuals studied). More specifically, the rs4988321(A) allele was associated with reduced lumbar spine BMD density (p = 3.3 x 10^-8), and femoral neck BMD (p = 3.8 x 10^-5). Note that rs3736228, another LRP5 SNP (also known as Ala1330Val), was independently associated with BMD in this same study. triallelic and on a chip [omim:OSTEOPOROSIS-PSEUDOGLIOMA SYNDROME]
95.0	rs2395029 (T;T)	common
			The rs2395029(T;T) genotype is the common genotype for this SNP, against which the rs2395029(T;G) and rs2395029(G;G) genotypes that are associated with reduced HIV viral load in HIV carriers are compared. See also rs9264942 and HIV.
			This SNP is thought to be involved in determining the HIV viral load set point during the asymptomatic period of infection. This SNP is estimated to explain 9.6% of the total variation in the viral set point. Humans show remarkable variation in vulnerability to infection by HIV-1 and especially in the clinical outcome following infection. One striking and largely unexplained difference is the level of circulating virus in the plasma during the non-symptomatic phase preceding progression to AIDS. This is known as the ''viral set point'' and can vary among individuals by as much as 4 to 5 logs. The HCP5 (HLA complex P5) gene is located 100 kb centromeric from HLAB on chromosome 6. HCP5 is a good candidate to interact with HIV-1, possibly through an antisense mechanism. Moreover, HCP5 is pred...
95.0	rs4987188 (G;G)

			[omim:MSH2 POLYMORPHISM]
95.0	rs1256049 (G;G)

			rs2234693 rs934079 and rs1256049 variations in ESR1 gene, in addition to the age of a woman, may predict the COH outcome in in vitro fertilization
95.0	rs964201 (G;G)

			rs964201 and rs2442496 arose approximately 50,000 years ago and show strong positive selection in the lineage leading to humans [http://originsgenomeresources.net/musings/?p=68]
95.0	rs2740574 (A;A)

			rs2740574(G) alleles are associated with an ~10 fold higher risk of aggressive prostate cancer in African American males. [PMID 16414488, OMIM [http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=124010
95.5	rs2032597 (A;A)

			[haplogroup:?]
96.6	rs2854344 (G;G)	1.25x risk of developing ovarian cancer

			associated with breast cancer risk and ovarian cancer More specifically: carriers of two rs2854344(A) alleles have a 25% reduced risk of developing ovarian cancer compared to carriers of two rs2854344(G) alleles, in a survey of ~5,000 women from the US, UK, and Denmark. showed '''no association''' with ovarian cancer risk 4,624 invasive epithelial ovarian cancer cases and 8,113 controls of white non-Hispanic origin ovarian cancer
96.6	rs6195 (A;A)

			[http://jcem.endojournals.org/cgi/content/abstract/92/8/3268 Abstract] linked to increased glucocorticoid sensitivity, coronary artery disease, and increased body mass index. [omim:GLUCOCORTICOID RECEPTOR POLYMORPHISM]
96.7	rs2229616 (G;G)	normal

			rs2229616, a variant in the MC4R gene known as V103I, has been associated with appetite regulation, body mass index (and thus obesity), and other features of metabolic syndrome. The most common allele is rs2229616(G); the rarer (A) allele encodes the 103I (isoleucine), and this (A) allele has been associated in a study of 8,000+ Caucasians with a significantly decreased waist circumference (1.46 cm, p = 0.020), decreased glycosylated hemoglobin (HbA1c) (0.09%, p = 0.040), and increased HDL-cholesterol (HDL-C) (+1.76 mg/dl, P = 0.056), but no change in blood pressure. The odds of having three or more components of the metabolic syndrome were substantially reduced among carriers of an rs2229616(A) allele (odds ratio = 0.46, p = 0.003). Basically, rs2229616(A) carriers are on average slight...
96.7	rs4987117 (C;C)

			This SNP, a variant in the BRCA2 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (T).
96.7	rs1800709 (C;C)

			[omim:BREAST CANCER]
96.7	rs3772534 (G;G)

			One report based on a study of 480 Danish families indicated that the rs3772534 SNP in the CBLB gene indicated an increased risk for developing type 1 diabetes, and that there might be co-inheritance with the rs3087243 SNP found in the CTLA4 gene. However, a subsequent study based on over 2,000 parent-child trios (ie families) failed to find any evidence of either effect.
96.7	rs17316729 (C;C)

			[haplogroup:?]
96.7	rs1799931 (G;G)

			rs1799931 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1799931(A).
98.2	rs11466023 (C;C)

			[omim:FAMILIAL MEDITERRANEAN FEVER]
98.3	rs11466024 (G;G)

			[omim:FAMILIAL MEDITERRANEAN FEVER]
98.3	rs268 (A;A)	normal risk

			rs268, a SNP in the lipoprotein lipase LPL gene, has been linked to increased susceptibility to idiopathic venous thromboembolism. A study of 300+ individuals resulted in an odds ratio of 3.09 (CI: 1.56-6.09, p=0.001) for carriers of a rs268(G) allele.
98.3	rs6025 (G;G)	normal/common

			rs6025 represents a SNP in the Factor V F5 gene, encoding a change in the protein from an arginine at position 506 to a glutamine. The resulting rs6025(A) allele encodes a mutation known as the Leiden mutation, R506Q, found in perhaps 3 to 5% of the individuals in most populations. About 1 in 10 individuals harboring the R506Q will experience clinically significant venous thromboembolism in their lifetimes (according to [http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=227400 OMIM]). Overall, the rs6025(A) allele appears to be necessary but not sufficient for the development of venous thromboembolism. Patients who are rs6025(A;G) heterozygotes but lack other risk-enhancing SNPs have a risk of recurrent deep venous thrombosis equal to patients with no such SNPs. In contrast, patients who ...
98.3	rs1800888 (C;C)

			[omim:BETA-2-ADRENORECEPTOR AGONIST, REDUCED RESPONSE TO]
98.3	rs5907 (G;G)

			[omim:HEPARIN COFACTOR II DEFICIENCY]
98.3	rs5352 (G;G)

			[omim:HIRSCHSPRUNG DISEASE 2]
98.3	rs1800750 (G;G)	higher acute otitis risk

			rs1800750, a SNP located at position -376 of the TNF gene, has been linked to increased risk for recurrent acute otitis in a study of 348 children. The (adjusted) odds ratio is 3.06 for (G;G) genotypes (p=0.07).
98.3	rs2075291 (C;C)	normal

			SNP rs2075291 represents a glycine to cysteine substitution at amino acid 185 of the APOA5 protein; it is also known as p.185Gly>Cys or c.553G>T. In both Chinese and non-Chinese Asians, the A allele (leading to the cysteine) is associated with higher risk for hypertriglyceridemia. The odds ratio is 4.45 (CI: 2.18-9.07, p<0.001). Heterozygosity was associated with a doubling of triglyceride levels, and all (11) rs2075291(A;A) homozygotes (as oriented relative to dbSNP, not as published) had severe hypertriglyceridemia (mean triglyceride level of 2292 +/- 447 mg/dl).
98.3	rs2308327 (A;A)	normal

			rs2308327, also known as K178R, is a SNP in the MGMT gene. The more common allele, rs2308327(A), encodes a lysine (K) at codon 178, while the (G) allele encodes an arginine (R). In a pooled analysis of 200+ lung cancer patients, the rs2308327(G) allele was reported to provide a protective effect against lung cancer, and furthermore, more (G) alleles meant more protection, particularly for smokers. The odds ratios reported (p=0.003) were 0.67 (CI: 0.45-1.01) for heterozygotes, and 0.10 (CI: 0.01-0.94) for rs2308327(G;G) homozygotes. In a study of 300+ colon cancer cases, rs2308327(G), in linkage disequilibrium with the previously reported MGMT Ile(143)Val SNP, had an inverse association with colorectal cancer risk (odds ratio 0.52, CI: 0.35-0.78, unadjusted p(trend) = 0.0003 for the additiv...
98.3	rs6063 (G;G)

			This is the first snp to experiment with the watson alignment. [omim:FIBRINOGEN MILANO XII, DIGENIC]
100.0	rs2032625 (G;G)

			[haplogroup:?]
100.0	rs2230500 (G;G)	normal risk

			A common SNP only in Asian populations, this SNP (also known as 1425G/A) and a close neighbor also in the PRKCH gene, rs3783799, have been associated with higher risk for subcortical silent brain infarction, a common form of stroke. In one study of ~1100 Japanese stroke patients, the odds ratio for carriers of the rs2230500(A) risk allele was reported as 1.40 (CI: 1.23-1.59, p=5x10e-7). A subsequent study reported the odds ratio for carriers of the (A) allele as 1.27 (CI: 1.09-1.48, p=0.0026) compared to individuals homozygous for rs2230500(G), based on studies of ~300 Japanese patients.
100.0	rs3092857 (A;A)

			[omim:B-CELL NON-HODGKIN LYMPHOMA, SOMATIC]
100.0	rs3848982 (G;G)

			[haplogroup:?]
100.0	rs2032627 (A;A)

			[haplogroup:?]
100.0	rs947267 (A;C)

			showed that rs947267 was significantly associated with schizophrenia rs778294 and rs947267 associated with the risk of schizophrenia, however rs947267, showed an opposite direction of genetic effect on schizophrenia risk here than in a previous study
100.0	rs11554290 (A;A)

			[omim:THYROID CARCINOMA, FOLLICULAR]
100.0	rs2032590 (T;T)

			[haplogroup:?]
100.0	rs17269816 (C;C)
			[haplogroup:O3]
			[haplogroup:?]
100.0	rs2032652 (T;T)
			[haplogroup:F-R]
			[haplogroup:?]
100.0	rs17107315 (T;T)

			[omim:PANCREATITIS, CHRONIC, SUSCEPTIBILITY TO]
100.0	rs2032665 (C;C)
			[haplogroup:F-R]
			[haplogroup:?]
100.0	rs17292650 (G;G)

			[omim:THROMBOCYTOSIS, SUSCEPTIBILITY TO]
100.0	rs2032593 (G;G)

			[haplogroup:?]
100.0	rs1799807 (A;A)

			[omim:APNEA, POSTANESTHETIC, DUE TO BCHE, ATYPICAL-1]
100.0	rs7483 (A;G)

			association of the rs7483 SNP with late-onset Alzheimer's disease
100.0	rs9786479 (T;T)

			[haplogroup:?]
100.0	rs2032667 (G;G)

			[haplogroup:?]
100.0	rs2032613 (A;A)

			[haplogroup:?]
100.0	rs11547328 (C;C)

			[omim:MELANOMA, CUTANEOUS MALIGNANT, 3]
100.0	rs1800443 (T;T)

			[omim:DOPAMINE RECEPTOR D4 POLYMORPHISM]
100.0	rs20320 (G;G)

			[haplogroup:?]
100.0	rs2032620 (G;G)

			[haplogroup:?]
100.0	rs2032654 (A;A)

			[haplogroup:?]
100.0	rs2032672 (A;A)

			[haplogroup:?]
100.0	rs2032639 (G;G)

			[haplogroup:?]
100.0	rs283413 (G;G)	common

			SNP rs283413, also known as G78stop, encodes a rare variant of the ADH1C gene that leads to a truncated alcohol dehydrogenase protein. These types of proteins are involved in detoxification and may be linked to neurodegenerative diseases. Originally identified in three Swedish patients with Parkinson's disease (PD), a study of ~1000 PD patients vs. ~1000 controls indicated an odds ratio for the risk allele of 3.25 (CI:1.31-8.05). [This risk is effectively for heterozygotes, since the risk allele is so rare that no homozygotes for it were observed.] In a study of 40 index cases, 10% were found to harbor the rs283413(T) risk allele.
100.0	rs16964465 (A;A)

			rs16964465 rs16964476 may influence the risk of obesity through possible regulation of hypothalamic neuropeptide secretion
100.0	rs13073139 (G;G)

			[omim:BIOTINIDASE DEFICIENCY]
100.0	rs2032606 (G;G)

			[haplogroup:?]
100.0	rs5917 (G;G)

			[omim:PEN(a)/PEN(b) ALLOANTIGEN POLYMORPHISM]
100.0	rs1800309 (G;G)

			[omim:ACID ALPHA-GLUCOSIDASE, ALLELE 4]
100.0	rs28989187 (G;G)

			[omim:MOSAIC VARIEGATED ANEUPLOIDY SYNDROME]
100.0	rs3218714 (C;C)

			[omim:CARDIOMYOPATHY, FAMILIAL HYPERTROPHIC, 1]
100.0	rs870849 (C;T)

			rs870849, a SNP in the LAG3 gene, has been associated with multiple sclerosis.
100.0	rs3924999 (C;T)

			a significant association between rs3924999 and Alzheimer's disease with psychosis
100.0	rs3899 (G;G)

			[haplogroup:?]
100.0	rs2032644 (T;T)

			[haplogroup:?]
100.0	rs4986893 (G;G)

			rs4986893 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*3 variant. This variant has been linked to poor metabolism of compounds like mephenytoin as well as proguanil, and it therefore has implications for malaria prophylaxis. [PMID 7969038, PMID 9093256] The risk allele is rs4986893(A). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (Prevacid). [omim:MEPHENYTOIN, POOR METABOLISM OF]
100.0	rs2228063 (A;A)

			[omim:CARBONIC ANHYDRASE II VARIANT]
100.0	rs28897672 (T;T)

			[omim:OVARIAN CANCER, SPORADIC]
100.0	rs2032658 (G;G)
			[haplogroup:R]
			[haplogroup:?]
100.0	rs16980558 (A;A)

			[haplogroup:?]
100.0	rs2032600 (A;A)

			[haplogroup:?]
100.0	rs3894 (C;C)

			[haplogroup:?]
100.0	rs7067279 (T;T)

			[haplogroup:?]
100.0	rs2032605 (C;C)

			[haplogroup:?]
100.0	rs3896 (C;C)

			[haplogroup:?]
100.0	rs2032601 (C;C)

			[haplogroup:?]
100.0	rs2032611 (A;A)

			[haplogroup:?]
100.0	rs26722 (C;C)

			[omim:PIGMENTATION OF HAIR, SKIN, AND EYES, VARIATION IN]
100.0	rs2032669 (T;T)

			[haplogroup:?]
100.0	rs2066702 (C;C)	alcoholism risk for African-Americans

			this [http://hmg.oxfordjournals.org/cgi/content/full/15/9/1539 paper] found significant association with rs2066702, the SNP that defines ADH1B3, in African-American families. Association was strongest with the ICD-10 definitions of alcoholism, with P=0.046 for PDTsum and 0.029 for PDTaverage; it was also significant for DSM-IV for PDTaverage (P=0.039). The high-risk allele was the C that encodes ADH1B1, and the low-risk allele encodes ADH1B*3 A review of the (at times conflicting) findings regarding ADH1B genotypes and maternal and fetal alcohol syndromes is available.[http://www.cdc.gov/genomics/hugenet/file/print/reviews/alcohol.pdf] [omim:ALCOHOL DEHYDROGENASE, BETA SUBUNIT, INDIANAPOLIS]
100.0	rs9786095 (C;C)
			[haplogroup:F-R]
			[haplogroup:?]
100.0	rs2032645 (A;A)

			[haplogroup:?]
100.0	rs2303790 (A;A)

			[omim:CHOLESTEROL ESTER TRANSFER PROTEIN DEFICIENCY]
100.0	rs28989181 (C;C)

			[omim:MOSAIC VARIEGATED ANEUPLOIDY SYNDROME]
100.0	rs3218713 (G;G)

			[omim:CARDIOMYOPATHY, FAMILIAL HYPERTROPHIC, 1]
100.0	rs17269928 (A;A)

			[haplogroup:?]
100.0	rs7014851 (T;T)

			[omim:ALOPECIA UNIVERSALIS CONGENITA]
100.0	rs3810710 (T;T)

			A (G) form of this SNP, located in exon 9 of the PDHA1 gene, has been observed in patients with pyruvate dehydrogenase E1 alpha deficiency . Deficiences in the PDHA gene may lead, to varying degrees, to lactic acidosis and/or neurological problems. [OMIM 312170, OMIM 300502] The traditional treatment for pyruvate deficiencies is a ketogenic diet, a type of diet very high in fat while low in carbohydrates. Medical supervision is considered essential. [omim:PYRUVATE DEHYDROGENASE E1-ALPHA DEFICIENCY]
100.0	rs9786191 (G;G)

			[haplogroup:?]
100.0	rs9786707 (C;C)
			[haplogroup:F-R]
			[haplogroup:?]
100.0	rs16990018 (A;A)

			[omim:SPONGIFORM ENCEPHALOPATHY WITH NEUROPSYCHIATRIC FEATURES]
100.0	rs2032621 (T;T)

			[haplogroup:?]
100.0	rs5742904 (G;G)

			[omim:HYPERCHOLESTEROLEMIA DUE TO LIGAND-DEFECTIVE APOLIPOPROTEIN B100]
100.0	rs16980426 (T;T)

			[haplogroup:?]
100.0	rs28989182 (G;G)

			[omim:MOSAIC VARIEGATED ANEUPLOIDY SYNDROME]
100.0	rs11540652 (G;G)

			[omim:LI-FRAUMENI SYNDROME 1]
100.0	rs2032666 (C;C)

			[haplogroup:?]
100.0	rs671 (G;G)	normal

			rs671 is a classic SNP, well known in a sense through the phenomena known as the 'alcohol flush', also known as the 'Asian Flush' or 'Asian blush', in which certain individuals, often of Asian descent, have their face, neck and sometimes shoulders turn red after drinking alcohol. The rs671(A) allele of the ALDH2 gene is the culprit, in that it encodes a form of the aldehyde dehydrogenase 2 protein that is defective at metabolizing alcohol. This allele is known as the ALDH*2 form, and individuals possessing either one or two copies of it show alcohol-related sensitivity responses including facial flushing, and severe hangovers (and hence they are usually not regular drinkers). Perhaps not surprisingly they appear to suffer less from alcoholism and alcohol-related liver disease. [PMID 511165...
100.0	rs5030849 (G;G)

			[omim:PHENYLKETONURIA, MILD]
100.0	rs16964476 (A;A)

			rs16964465 rs16964476 may influence the risk of obesity through possible regulation of hypothalamic neuropeptide secretion
100.0	rs2032636 (G;G)

			[haplogroup:?]
100.0	rs28374544 (A;A)

			[omim:TETRALOGY OF FALLOT]
100.0	rs16981293 (C;C)

			[haplogroup:?]
100.0	rs2032663 (C;C)

			[haplogroup:?]
100.0	rs16980548 (C;C)

			[haplogroup:?]
100.0	rs17158558 (C;C)

			[omim:HIRSCHSPRUNG DISEASE]
100.0	rs2032648 (T;T)

			[haplogroup:?]
100.0	rs2227945 (A;A)

			This SNP, a variant in the BRCA1 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (G).
100.0	rs8192466 (C;C)

			[omim:CENTRAL HYPOVENTILATION SYNDROME, CONGENITAL]
100.0	rs17073260 (C;C)

			[omim:ARTHROPATHY, PROGRESSIVE PSEUDORHEUMATOID, OF CHILDHOOD]
100.0	rs11971167 (G;G)

			[omim:VAS DEFERENS, CONGENITAL BILATERAL ABSENCE OF]
100.0	rs2032643 (T;T)

			[haplogroup:?]
100.0	rs28989186 (C;C)

			[omim:MOSAIC VARIEGATED ANEUPLOIDY SYNDROME]
100.0	rs3902 (A;A)

			[haplogroup:?]
100.0	rs3911 (A;A)

			[haplogroup:?]
100.0	rs1801279 (G;G)

			rs1801279 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1801279(A).
100.0	rs2032603 (A;A)

			[haplogroup:?]
100.0	rs2032612 (C;C)

			[haplogroup:?]
100.0	rs28989185 (T;T)

			[omim:MOSAIC VARIEGATED ANEUPLOIDY SYNDROME]
100.0	rs9785908 (G;G)
			[haplogroup:F-R]
			[haplogroup:?]
100.0	rs11555096 (G;G)

			[omim:FUMARYLACETOACETASE PSEUDODEFICIENCY]
100.0	rs2032599 (T;T)

			[haplogroup:?]
100.0	rs2032649 (T;T)

			[haplogroup:?]
100.0	rs2032617 (G;G)

			[haplogroup:?]
None	rs28399653 (G;G)

			[omim:LUTHERAN BLOOD GROUP POLYMORPHISM Lu(a)/Lu(b)]
None	rs28929497 (T;T)

			[omim:HEMOLYTIC UREMIC SYNDROME, ATYPICAL]
None	rs28936397 (T;T)

			[omim:BRACHYDACTYLY, TYPE C]
None	rs28934877 (A;A)

			[omim:CRIGLER-NAJJAR SYNDROME, TYPE II]
None	rs9341308 (A;A)

			[haplogroup:?]
None	rs13447354 (G;G)

			[haplogroup:?]
None	rs28928896 (T;T)

			During some blast and clustalw analysis of the watson genome, this snp is an outlier. It appears to occur in a fairly well conserved region, which appears slightly differently at several places in the genome. [omim:STEATOCYSTOMA MULTIPLEX]
None	rs28937904 (G;G)

			[omim:MUSCULAR DYSTROPHY, CONGENITAL, 1C, WITH NEUROLOGIC ABNORMALITIES]
None	rs28936682 (G;G)

			[omim:DEJERINE-SOTTAS SYNDROME, AUTOSOMAL RECESSIVE]
None	rs28934607 (G;G)

			[omim:VITAMIN D-DEPENDENT RICKETS, TYPE I]
None	rs28929474 (C;C)

			[omim:PI Z(AUGSBURG)]
None	rs28936670 (G;G)

			[omim:TETRALOGY OF FALLOT]
None	rs28937580 (C;C)

			[omim:SYMPHALANGISM, PROXIMAL]
None	rs28933676 (T;T)

			[omim:HEMOPHILIA A]
None	rs28936694 (C;C)

			[omim:GLAUCOMA 1, OPEN ANGLE, A, DIGENIC]
None	rs2066847 (D;D)

			linked to Crohn's disease
None	rs28933390 (C;C)

			[omim:BCHE, FLUORIDE 2]
None	rs5744168 (G;G)

			[omim:LEGIONNAIRE DISEASE, SUSCEPTIBILITY TO]
None	rs1800787 (C;C)

			rs1800787(T;T) homozygotes are at 6 fold higher risk compared to (C;C) homozygotes or (C;T) heterozygotes for carotid atherosclerosis . This polymorphism is known as the 'C148-T' variant, and is located in at the '-148' position of the FGB gene, also known as beta fibrinogen. Note: due to inconsistencies between databases and the literature, the association of this rs# with this polymorphism name as published is highly likely but not guaranteed.
None	rs7067483 (T;T)

			[haplogroup:?]
None	rs28931584 (C;C)

			[omim:SPHEROCYTOSIS, HEREDITARY]
None	rs28935470 (C;C)

			[omim:OTOPALATODIGITAL SYNDROME, TYPE II]
None	rs28937318 (C;C)

			[omim:BRUGADA SYNDROME]
None	rs28937569 (C;C)

			[omim:NEURONOPATHY, DISTAL HEREDITARY MOTOR, TYPE IIB]
None	rs28928909 (G;G)

			[omim:MYOPATHY, CENTRONUCLEAR, MILD]
None	rs28937891 (G;G)

			[omim:WOLFRAM SYNDROME]
None	rs28931614 (G;G)

			[omim:ACHONDROPLASIA]
None	rs28937903 (C;C)

			[omim:MUSCULAR DYSTROPHY, CONGENITAL, 1C, WITH NEUROLOGIC ABNORMALITIES]
None	rs28934611 (A;A)

			[omim:OPITZ SYNDROME, X-LINKED]
None	rs28930074 (A;A)

			[omim:CORTICOSTERONE METHYLOXIDASE TYPE I DEFICIENCY]
None	rs28933386 (T;T)

			[omim:NOONAN SYNDROME 1]
None	rs28937868 (C;C)

			[omim:CARDIOENCEPHALOMYOPATHY, FATAL INFANTILE, DUE TO CYTOCHROME c OXIDASE DEFICIENCY]
None	rs28933402 (C;C)

			[omim:LEIGH SYNDROME DUE TO CYTOCHROME c OXIDASE DEFICIENCY]
None	rs2267802 (A;A)

			[haplogroup:?]
None	rs28935477 (G;G)

			[omim:IMMUNODYSREGULATION, POLYENDOCRINOPATHY, AND ENTEROPATHY, X-LINKED]
None	rs9341296 (C;C)

			[haplogroup:?]
None	rs28937897 (A;A)

			[omim:ESOPHAGEAL SQUAMOUS CELL CARCINOMA, SOMATIC]
None	rs34043621 (T;T)

			[haplogroup:?]
None	rs28934590 (C;C)

			[omim:C2 DEFICIENCY, TYPE II]
None	rs28937575 (G;G)

			[omim:HYPOTHYROIDISM, ATHYROIDAL, WITH SPIKY HAIR AND CLEFT PALATE]
None	rs28931598 (C;C)

			[omim:OCULODENTODIGITAL DYSPLASIA]
None	rs28934588 (A;A)

			[omim:BOMBAY PHENOTYPE]
None	rs28934571 (C;C)

			[omim:HEPATOCELLULAR CARCINOMA]
None	rs28933373 (A;A)

			[omim:TOOTH AGENESIS, SELECTIVE, 3]
None	rs9341314 (G;G)

			[haplogroup:?]
None	rs17879961 (A;A)

			This SNP, a variant in the CHEK2 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (C). rs17879961 one of 3 SNPs associated with increased risk of lung cancer
None	rs16980360 (G;G)

			[haplogroup:?]
None	rs28936697 (G;G)

			[omim:PEROXISOME BIOGENESIS DISORDER, COMPLEMENTATION GROUP 3]
None	rs3800373 (A;A)

			rs9296158 rs3800373 rs1360780 rs9470080 linked with the severity of child abuse to predict level of adult PTSD symptoms after correcting for multiple testing.
None	rs28928868 (G;G)

			[omim:HYPOCHONDROPLASIA]
None	rs1800460 (C;C)

			rs1800460 is a SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP is rs1800460(T), and it encodes the TPMT*3A allele. While still rare, it is more common in Caucasians (4.5% of all alleles) than in African-Americans (0.8%).
None	rs28999114 (A;A)

			[omim:PROGRESSIVE EXTERNAL OPHTHALMOPLEGIA WITH MITOCHONDRIAL DNA DELETIONS, AUTOSOMAL DOMINANT, 2]
None	rs28936673 (A;A)

			[omim:CARNITINE PALMITOYLTRANSFERASE II DEFICIENCY, INFANTILE]
None	rs28939094 (A;A)

			[omim:SPASTIC PARAPLEGIA 3, AUTOSOMAL DOMINANT]
None	rs28936416 (A;A)

			[omim:PITUITARY HORMONE DEFICIENCY, COMBINED, HESX1-RELATED]
None	rs2032641 (C;C)

			[haplogroup:?]
None	rs708272 (G;G)

			rs708272, also known as the Taq1B polymorphism of the CETP gene, may influence the levels of the 'good' cholestorols, the high density lipoprotein (HDL) cholesterols. Generally, the B2 allele is considered to lead to higher HDL levels. However, high HDL cholesterol, at least when combined with another HDL raising SNP (rs1800588), doesn't appear to actually protect individuals from coronary artery disease, at least based on one study of ~800 Caucasian male patients. [PMID 18164013
None	rs28939378 (G;G)

			[omim:CONGENITAL DISORDER OF GLYCOSYLATION, TYPE Ik]
None	rs28934574 (G;G)

			[omim:OSTEOSARCOMA]
None	rs17307294 (A;A)

			[haplogroup:?]
None	rs361525 (G;G)	complex; generally normal risk

			rs361525 is also known as the TNF -238 SNP, and occasionally the rs361525(A) allele is referred to as 238.2 (with the more common (G) allele being 238.1). This SNP has been linked to a wide variety of conditions: * A large study of over 5,000 Caucasian women found that rs361525(A) allele carriers were at somewhat elevated risk for breast cancer compared to the (G;G) genotype, with an odds ratio per allele of 1.18, CI: 1.04-1.35, p(trend)= 0.008. * A study of ~100 allogeneic haematopoietic stem cell transplant recipients in Brazil concludes that graft versus host disease (GVHD) is about twice as frequent if either the donor or the recipient are rs361525(A) carriers. * Children who are rs361525(G;G) homozygotes may be more prone to ear infections; adjusted odds ratio 2.29, p=0.03). * The rs3...
None	rs28933675 (G;G)

			[omim:HEMOPHILIA A]
None	rs28933997 (G;G)

			[omim:MALIGNANT HYPERTHERMIA, SUSCEPTIBILITY TO, 1]
None	rs28937295 (C;C)

			[omim:HEMOPHILIA A]
None	rs28940572 (C;C)

			[omim:P BLOOD GROUP SYSTEM, p PHENOTYPE]
None	rs28937887 (G;G)

			[omim:PROGRESSIVE EXTERNAL OPHTHALMOPLEGIA WITH MITOCHONDRIAL DNA DELETIONS, DIGENIC]
None	rs17855739 (C;C)

			[omim:FUCOSYLTRANSFERASE-6 DEFICIENCY, PLASMA, INDONESIAN TYPE]
None	rs28933376 (G;G)

			[omim:HEMOPHAGOCYTIC LYMPHOHISTIOCYTOSIS, FAMILIAL, 2]
None	rs28940880 (G;G)

			[omim:ALBINISM, OCULOCUTANEOUS, TYPE IA]
None	rs28933400 (T;T)

			[omim:MIGRAINE, FAMILIAL HEMIPLEGIC, 2]
None	rs1008805 (G;G)

			the presence of at least one G allele at rs1008805 was significantly associated with an increase in the risk of breast cancer (OR = 1.72 [95% CI, 1.20-2.49]), especially with estrogen and progesterone receptor negative breast cancer (OR = 3.89 [1.74-8.70] and OR = 2.52 [1.26-5.05], respectively).
None	rs28935480 (C;C)

			[omim:PROPERDIN DEFICIENCY, TYPE I]
None	rs28940302 (G;G)

			[omim:WARFARIN RESISTANCE]
None	rs28940300 (C;C)

			[omim:ERYTHROCYTOSIS, FAMILIAL, 2]
None	rs9341301 (T;T)

			[haplogroup:?]
None	rs28933379 (G;G)

			[omim:GASTRIC CANCER, SOMATIC]
None	rs28933396 (G;G)

			[omim:CENTRAL CORE DISEASE]
None	rs28937881 (C;C)

			[omim:HYPOPHOSPHATEMIC RICKETS, AUTOSOMAL DOMINANT]
None	rs28937582 (T;T)

			[omim:BLOOD GROUP--P SYSTEM, P(k) ANTIGEN]
None	rs28934570 (G;G)

			[omim:TRIOSEPHOSPHATE ISOMERASE DEFICIENCY]
None	rs28941768 (G;G)

			[omim:GLUTAMATE FORMIMINOTRANSFERASE DEFICIENCY]
None	rs28931582 (T;T)

			[omim:ACROMESOMELIC DYSPLASIA, MAROTEAUX TYPE]
None	rs9786153 (T;T)
			[haplogroup:R1b1c]
			[haplogroup:?]
None	rs13447352 (A;A)

			[haplogroup:?]
None	rs28933368 (G;G)

			[omim:GLIOBLASTOMA, SOMATIC]
None	rs28933384 (G;G)

			[omim:JERVELL AND LANGE-NIELSEN SYNDROME]
None	rs28936704 (T;T)

			[omim:GROWTH HORMONE DEFICIENCY, HESX1-RELATED]
None	rs28937872 (G;G)

			[omim:ECTODERMAL DYSPLASIA, HIDROTIC]
None	rs28937889 (T;T)

			[omim:MAL DE MELEDA]
None	rs182549 (C;T)

			Also known as 'G/A(-22018)' and located in the MCM6 but with influence on the lactase LCT gene, rs182549 is one of two SNPs that is associated with the primary haplotype associated with hypolactasia, more commonly known as lactose intolerance in European Caucasian populations. [PMID 11788828, PMID 15114531] In these populations, the rs182549(C) allele (as named in accordance with dbSNP) is both the more common allele and the one associated with lactose intolerance. In populations of sub-Saharan Africans, though, the rs182549(C) allele is unlikely to be predictive of lactose intolerance, and other SNPs are predictive instead. [PMID 15106124, PMID 17159977] * See also [http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=601806&a=601806_AllelicVariant0002 OMIM 601806.0002]
None	rs1015362 (T;T)	(?)normal

			rs1015362 is a SNP near the ASIP (agouti signaling protein) gene on chromosome 20. This SNP is one of a tightly-linked pair that increases the likelihood of an individual being prone to sun sensitivity, in other words, freckles and sunburn, based on a study of 6,000+ Caucasians (5,000+ Icelanders + 1,000+ Dutch). The odds ratios, presumably on a dominant basis, and at least in the largest population (Icelanders) for 'freckles and burns vs. no freckles and tans' for the haplotype pair rs1015362(G) - rs4911414(T) is 3.91 (CI: 2.54-6.03) for males and 2.42 (CI: 1.52-3.86) for females, with an overall p=0.051. Based on a study by the same authors of 4,000+ skin cancer patients, this haplotype was seen to confer significant increased risk for cutaneous malignant melanoma (odds ratio 1.45, p = 1...
None	rs28933397 (C;C)

			[omim:MALIGNANT HYPERTHERMIA, SUSCEPTIBILITY TO, 1]
None	rs908832 (G;G)	normal
			This is the genotype of User:Watson
			This SNP, a synonymous substitution in the ABCA2 gene, has been linked to early onset Alzheimer's disease with an odds ratio of 3.8 for disease development in carriers of the A allele (in dbSNP orientation) compared to controls (95% CI 2-7.3), based on a study of ~400 Caucasian patients. Subsequently, this association was replicated in a Western European population (n=291, p=0.008), but not in a second sample from Southern Europe. rs908832 was not polymorphic in a Japanese sample. Furthermore, rs908832 was not associated with either serum cholesterol levels or with the risk for coronary artery disease, but did seem to be related to cholesterol levels in the cerebrospinal fluid.
None	rs1236440 (C;C)

			[haplogroup:?]
None	rs28931605 (G;G)

			[omim:CATARACT, CONGENITAL LAMELLAR]
None	rs28940879 (G;G)

			[omim:ALBINISM, OCULOCUTANEOUS, TYPE IA]
None	rs28935172 (C;C)

			[omim:LISSENCEPHALY, X-LINKED]
None	rs9786357 (G;G)

			[haplogroup:?]
None	rs28937890 (C;C)

			[omim:WOLFRAM SYNDROME]
None	rs13447353 (C;C)

			[haplogroup:?]
None	rs2032637 (A;A)

			[haplogroup:?]
None	rs28937596 (T;T)

			[omim:LEUKOENCEPHALOPATHY WITH VANISHING WHITE MATTER]
None	rs9341317 (T;T)
			[haplogroup:CR]
			[haplogroup:?]
None	rs6046 (G;G)

			[omim:MYOCARDIAL INFARCTION, DECREASED SUSCEPTIBILITY TO]
None	rs7067478 (A;A)
			[haplogroup:R1]
			[haplogroup:?]
None	rs279871 (T;T)

			This SNP in the GABRA2 gene has been linked to Alcoholism. The strongest association for this SNP is seen when it is a member of a haplotype consisting of the rs279871(A) + rs279845(T) + rs279836(A) alleles .
None	rs28931593 (C;C)

			[omim:KERATODERMA, PALMOPLANTAR, WITH DEAFNESS]
None	rs28937315 (T;T)

			[omim:RUBINSTEIN-TAYBI SYNDROME, INCOMPLETE]
None	rs28939075 (T;T)

			[omim:EPILEPSY, LATERAL TEMPORAL LOBE, AUTOSOMAL DOMINANT]
None	rs28935474 (G;G)

			[omim:CHONDRODYSPLASIA PUNCTATA 1, X-LINKED RECESSIVE]
None	rs28937871 (T;T)

			[omim:COLON CANCER, HEREDITARY NONPOLYPOSIS, TYPE 7]
None	rs5219 (C;C)	normal

			The association between type-1 diabetes and rs5219 is mentioned as being replicated in ; there is also a 90% correlation between rs5219 and rs5215. This SNP is one of 4 relatively common SNPs reported to represent risk for type-2 diabetes in the DESIR prospective study of 3,877 Caucasian participants. Under an additive model, the odds ratio for the minor (risk) allele (T) is 1.15 (CI: 0.95-1.4, p=0.2, ie not significant). But for the 4 SNPs, each risk allele increased type-2 diabetes risk by 1.34x (p=2x10e-6), with an odds ratio of 2.48 (CI: 1.59-3.86) for carriers of 4 or more compared to those with one or none (risk alleles). significantly associated p = 0.0034; in 1,630 Japanese subjects with type-2 diabetes and in 1,064 controls
None	rs28940579 (A;A)

			[omim:FAMILIAL MEDITERRANEAN FEVER]
None	rs16980502 (C;C)

			[haplogroup:?]
None	rs28933382 (C;C)

			[omim:MYOKYMIA]
None	rs1800401 (G;G)	(?)blue/gray eyes possible

			rs1800401 is located in exon 7 of the OCA2 gene at amino acid position 305. The (T) allele encodes the amino acid tryptophan (instead of arginine), and it is one of several SNPs associated with increased odds of having brown or black eye color in Caucasians. One copy of of rs1800401(T) is sufficient for this effect. [PMID 12163334, PMID 15889046; [http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=203200&a=203200_AllelicVariant0011 OMIM 203200.0011
None	rs793862 (G;G)	common

			Rs793862, a SNP in the DCDC2 gene, is in a region that crops up in several independent studies as likely to associated with dyslexia. The risk allele in the Caucasian populations studied is (A). One study reports that the odds ratio for rs793862 genotypes increases if calculated from subsets of more severely dyslexic individuals as compared to more heterogenous, larger groups of dyslexic individuals. The genotype relative risk (GRR) for rs793862(A;A) increased from 3.15 (95% CI 1.307.66; P=.011) for the larger group up to 5.40 (95% CI 1.2723.01; P=.002) for the most severely affected group. Combined with another SNP marker in the DCDC2 gene, rs807701, the (haplotype) GRR also increased for the homozygous haplotype A-C, from 4.11 (95% CI 2.776.08; P<.0001) for the larger group, up to 11...
None	rs3188996 (A;A)

			[omim:PAX8 POLYMORPHISM]
None	rs28928876 (C;C)

			[omim:HEMOGLOBIN M (IWATE)]
None	rs2032623 (D;D)

			[haplogroup:?]
None	rs28933399 (T;T)

			[omim:MIGRAINE, FAMILIAL HEMIPLEGIC, 2]
None	rs16980473 (C;C)

			[haplogroup:?]
None	rs9786502 (T;T)
			[haplogroup:F-R]
			[haplogroup:?]
None	rs28940310 (C;C)

			[omim:TRANSPOSITION OF THE GREAT ARTERIES, DEXTRO-LOOPED]
None	rs28730837 (G;G)

			[omim:MYELOPEROXIDASE DEFICIENCY]
None	rs28933693 (C;C)

			[omim:MUSCULAR DYSTROPHY, LIMB-GIRDLE, TYPE 2D]
None	rs28933684 (G;G)

			[omim:EXUDATIVE VITREORETINOPATHY, X-LINKED]
None	rs28936072 (T;T)

			[omim:HOYERAAL-HREIDARSSON SYNDROME]
None	rs28940897 (T;T)

			[omim:NIEMANN-PICK DISEASE, TYPE C1]
None	rs17860403 (C;C)

			[omim:AUTOIMMUNE LYMPHOPROLIFERATIVE SYNDROME, TYPE IIA]
None	rs17848368 (G;G)

			[omim:OBESITY, SEVERE, AND TYPE II DIABETES]
None	rs28928893 (A;A)

			[omim:EPIDERMOLYSIS BULLOSA SIMPLEX, DOWLING-MEARA TYPE]
None	rs2032602 (T;T)

			[haplogroup:?]
None	rs28940571 (G;G)

			[omim:P BLOOD GROUP SYSTEM, p PHENOTYPE]
None	rs16980621 (A;A)

			[haplogroup:?]
None	rs28931589 (G;G)

			[omim:HEPATOBLASTOMA, SOMATIC]
None	rs34078768 (G;G)

			[haplogroup:?]
None	rs28942075 (C;C)

			[omim:WILSON DISEASE]
None	rs28929478 (G;G)

			[omim:DARIER DISEASE]
None	rs28934608 (C;C)

			[omim:FACTOR XI DEFICIENCY]
None	rs28935174 (G;G)

			[omim:CHONDRODYSPLASIA PUNCTATA 2, X-LINKED DOMINANT]
None	rs28936684 (G;G)

			[omim:HYPERPARATHYROIDISM, NEONATAL SEVERE PRIMARY]
None	rs28940886 (C;C)

			[omim:LCAT DEFICIENCY]
None	rs28937894 (C;C)

			[omim:DEAFNESS, AUTOSOMAL DOMINANT NONSYNDROMIC SENSORINEURAL 6]
None	rs28931591 (G;G)

			[omim:EPILEPSY, NOCTURNAL FRONTAL LOBE, TYPE 1]
None	rs28929485 (G;G)

			[omim:KERATITIS-ICHTHYOSIS-DEAFNESS SYNDROME]
None	rs28937590 (A;A)

			[omim:GRACILE SYNDROME]
None	rs28934880 (C;C)

			[omim:3-@BETA-HYDROXYSTEROID DEHYDROGENASE, TYPE II, DEFICIENCY OF]
None	rs29001637 (C;C)

			[omim:RETINITIS PIGMENTOSA 4]
None	rs17306699 (A;A)

			[haplogroup:?]
None	rs28928870 (G;G)

			[omim:OVARIAN HYPERSTIMULATION SYNDROME]
None	rs28931599 (C;C)

			[omim:OCULODENTODIGITAL DYSPLASIA]
None	rs28931601 (G;G)

			[omim:OCULODENTODIGITAL DYSPLASIA]
None	rs2606345 (A;A)

			577 testicular germ cell tumors cases (254 seminoma, 323 nonseminoma) and 707 controls. inversely associated with nonseminoma: rs4886605 OR = 0.75 (95% CI = 0.54-1.04) among the heterozygotes and OR = 0.37, 95% CI = 0.12-1.11 among the homozygotes with a p-value for trend = 0.02; rs2606345 OR = 0.69 (95% CI = 0.51-0.93) among heterozygotes and OR = 0.70 (95% CI = 0.42-1.17) among homozygotes, with a p-value for trend = 0.02.
None	rs2268588 (A;A)

			[haplogroup:?]
None	rs2032616 (C;C)

			[haplogroup:?]
None	rs2814778 (T;T)

			rs2814778 is within the DARC gene, which encodes the Duffy blood group antigen . This SNP shows an almost perfectly fixed difference in frequency between Europeans and those with African ancestry. [One exception appears to be a certain population of Czech gypsies, and certain non-Ashkenazi Jewish populations.]. Additionally the Namibian San samples of the CEPH-HGDP are, uncharacteristically for Africans, all AA homozygotes for this SNP. The rs2814778 (G) allele is associated with African populations, while rs2814778 (A) is associated with European populations and south-western Native American populations.
None	rs28933081 (G;G)

			[omim:OROFACIAL CLEFT 5]
None	rs612709 (G;G)

			rs612709, a SNP in the ADAM33 gene, has been linked to a predisposition to asthma and bronchial hyperresponsiveness. [PMID 12110844, PMID 14564349]
None	rs17307398 (T;T)
			[haplogroup:R]
			[haplogroup:?]
None	rs16906252 (C;C)

			strongly associated with MGMT methylation (multivariate odds ratio 18.0; 95% confidence interval, 6.2-52.1, P < 0.0001) and loss of MGMT expression in colorectal cancer tumors
None	rs28940887 (G;G)

			[omim:LCAT DEFICIENCY]
None	rs2267801 (T;T)

			[haplogroup:?]
None	rs2319818 (G;G)

			[haplogroup:?]
None	rs28928908 (C;C)

			[omim:AMEGAKARYOCYTIC THROMBOCYTOPENIA, CONGENITAL]
None	rs28934580 (C;C)

			[omim:SEGAWA SYNDROME, AUTOSOMAL RECESSIVE]
None	rs3913 (-;-)

			[haplogroup:?]
None	rs1805006 (C;C)

			rs1805006, known as Asp84Glu or D84E, is one of several SNPs in the MC1R gene associated with higher risk of melanoma. The risk allele is rs1805006(A), compared with the wild-type rs1805006(C) allele. See also [http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=155555&a=155555_AllelicVariant0003 OMIM 155555.0003]
None	rs28940884 (T;T)

			[omim:GALACTOSE EPIMERASE DEFICIENCY]
None	rs28940892 (T;T)

			[omim:GLUCOCORTICOID DEFICIENCY 1]
None	rs28933098 (G;G)

			[omim:MYOPATHY, MYOSIN STORAGE]
None	rs2279744 (G;G)

			rs2279744, a variant in the promoter of the MDM2 also known as '-410T-G' and 'SNP309', has been studied for several years to determine it's role in cancer origin and treatment. The interest primarily stems from the ability of the MDM2 protein to bind to and thereby enhance the degradation of the tumor suppressor protein known as p53. Studies on rs2279744 include: * rs2279744(G) carriers in individuals with cancer tend to develop such cancers on average 12 years earlier than those lacking this allele, and the frequency of rs2279744(G) was greatly increased in those who developed soft tissue sarcomas at a young age. * Individuals with one or more rs2279744(G) alleles who are also carriers of the TP53 rs1042522(C) (arg at aa72) SNP tend to develop cancers earlier than rs2279744(T;T) homozygo...
None	rs9341278 (G;G)

			[haplogroup:?]
None	rs9786184 (C;C)

			[haplogroup:?]
None	rs28935473 (G;G)

			[omim:MELNICK-NEEDLES SYNDROME]
None	rs28928898 (A;A)

			[omim:PACHYONYCHIA CONGENITA, TYPE 2]
None	rs28933398 (T;T)

			[omim:MIGRAINE, FAMILIAL HEMIPLEGIC, 2]
None	rs28940303 (T;T)

			[omim:WARFARIN RESISTANCE]
None	rs2254958 (-;-)

			While the ApoE4 allele (rs429358(C)) is widely accepted as the predominant genetic risk factor for Alzheimer's disease, there are likely to be numerous other factors, both genetic and environmental, associated to lesser degrees with susceptibility to the disease. Genes influencing the immune system, and in particular susceptibility to viral infections such as herpes, may be among such factors. This SNP, located in the promoter region of the EIF2AK2 gene and thus implicated in the activation of HIV and HSV-1 viruses, is seen more commonly in ~300 Alzheimer patients than in the same number of controls. The risk allele is rs2254958(C). The odds ratio is reported to be 1.61 (CI: 1.02-2.55) for rs2254958(C;C) homozygotes, and 1.24 (CI: 0.80-1.93) for rs2254958(C;T) heterozygotes, compared with...
None	rs28934001 (C;C)

			[omim:MALIGNANT HYPERTHERMIA, SUSCEPTIBILITY TO, 1]
None	rs1805008 (C;C)

			rs1805008, known as Arg160Trp or R160W, is one of several SNPs in the MC1R gene associated with red hair (redheads), in this case in an Irish population although this has also been reported in Icelandic and Dutch populations . The risk allele is rs1805008(T), compared with the wild-type rs1805008(C) allele. [http://yannklimentidis.blogspot.com/2008/02/mc1r-genotypes-skin-cancer-risk-and.html blog] about designing melanocortin analogs specific to these genotypes. See also [http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=155555&a=155555_AllelicVariant0005 OMIM 155555.0005]
None	rs3803300 (C;C)

			G allele associated with schizophrenia
None	rs28931600 (G;G)

			[omim:SYNDACTYLY, TYPE III]
None	rs28934609 (C;C)

			[omim:FACTOR XI DEFICIENCY]
None	rs4911414 (T;T)	2-4x higher risk of sun sensitivity if part of risk haplotype

			rs4911414 is a SNP near the ASIP (agouti signaling protein) gene on chromosome 20. This SNP is one of a tightly-linked pair that increases the likelihood of an individual being prone to sun sensitivity, in other words, freckles and sunburn, based on a study of 6,000+ Caucasians (5,000+ Icelanders + 1,000+ Dutch). The odds ratios, presumably on a dominant basis, and at least in the largest population (Icelanders) for 'freckles and burns vs. no freckles and tans' for the haplotype pair rs1015362(G) - rs4911414(T) is 3.91 (CI: 2.54-6.03) for males and 2.42 (CI: 1.52-3.86) for females, with an overall p=0.051. Based on a study by the same authors of 4,000+ skin cancer patients, this haplotype was seen to confer significant increased risk for cutaneous malignant melanoma (odds ratio 1.45, p = 1...
None	rs28936674 (G;G)

			[omim:CARNITINE PALMITOYLTRANSFERASE II DEFICIENCY, INFANTILE]
None	rs28940304 (A;A)

			[omim:WARFARIN RESISTANCE]
None	rs28934887 (C;C)

			[omim:PROPIONIC ACIDEMIA]
None	rs28939680 (G;G)

			[omim:CHARCOT-MARIE-TOOTH DISEASE, AXONAL, TYPE 2F]
None	rs28936671 (G;G)

			[omim:CHOREA, BENIGN HEREDITARY]
None	rs9786197 (C;C)
			[haplogroup:R1]
			[haplogroup:?]
None	rs28940883 (T;T)

			[omim:GALACTOSE EPIMERASE DEFICIENCY]
None	rs28928884 (C;C)

			[omim:HEMOGLOBIN CHAROLLES]
None	rs28940896 (G;G)

			[omim:PALMOPLANTAR KERATODERMA, EPIDERMOLYTIC, WITH KNUCKLE PADS]
None	rs28999112 (G;G)

			[omim:DEAFNESS, AUTOSOMAL DOMINANT 20]
None	rs28937884 (A;A)

			[omim:BLEPHAROPHIMOSIS, PTOSIS, AND EPICANTHUS INVERSUS, TYPE I]
None	rs28933087 (A;A)

			[omim:PACHYONYCHIA CONGENITA, TYPE 1]
None	rs28937909 (G;G)

			[omim:GLYCOGEN STORAGE DISEASE II, ADULT FORM]
None	rs13447347 (G;G)
			[haplogroup:BR]
			[haplogroup:?]
None	rs28937597 (C;C)

			[omim:MUSCULAR DYSTROPHY, LIMB-GIRDLE, TYPE 1A]
None	rs2032642 (I;I)

			[haplogroup:?]
None	rs28933100 (C;C)

			[omim:ECTODERMAL DYSPLASIA, ANHIDROTIC, WITH T-CELL IMMUNODEFICIENCY, AUTOSOMAL DOMINANT]
None	rs28935478 (T;T)

			[omim:HYPOAGAMMAGLOBULINEMIA, X-LINKED]
None	rs2032664 (C;C)

			[haplogroup:?]
None	rs28937906 (C;C)

			[omim:CHARCOT-MARIE-TOOTH DISEASE, RECESSIVE INTERMEDIATE A]
None	rs28934904 (G;G)

			[omim:RETT SYNDROME]
None	rs6449213 (T;T)	~4x higher risk for hyperuracemia

			This is basically a surrogate for rs7442295, and thus associated with higher serum urate levels.
None	rs34276300 (C;C)

			[http://www.jogg.info/41/Turner.htm] Since R1b1c is very common, the first interesting discovery involved a SNP in that haplogroup, rs34276300, which was found to be ancestral in one branch of R1b1c and derived in several other branches. [http://dna-forums.org/index.php?showtopic=2909&pid=42643&st=40 dna-forums.org] discussion
None	rs1047286 (C;T)

			[omim:C3 POLYMORPHISM, HAV 4-1 PLUS/MINUS TYPE]
None	rs28934591 (C;C)

			[omim:APPARENT MINERALOCORTICOID EXCESS, HYPERTENSION DUE TO]
None	rs28933685 (T;T)

			[omim:NORRIE DISEASE]
None	rs28931570 (G;G)

			[omim:PI I]
None	rs28934573 (G;G)

			[omim:HEPATOBLASTOMA]
None	rs16980478 (C;C)
			[haplogroup:F-R]
			[haplogroup:?]
None	rs28942114 (T;T)

			[omim:FACTOR V AND FACTOR VIII, COMBINED DEFICIENCY OF]
None	rs2241766 (T;T)

			breast cancer. 733 hospital-based breast cancer cases and 839 controls rs2241766(T;G): OR, 0.61; 95% CI, 0.46-0.80 rs1501299(G;G): odd ratios (OR), 1.80; 95% confidence interval (95% CI), 1.14-2.85; *rs7539542 associated with breast cancer risk (OR, 0.51; 95% CI, 0.28-0.92) when compared with high signalers, intermediate signalers had a 4.16-fold increase in breast cancer risk (95% CI, 0.49-35.19), and low signalers had a 6.56-fold increase in breast cancer risk (95% CI, 0.78-54.89; P(trend) = 0.001).
None	rs28940578 (C;C)

			[omim:FAMILIAL MEDITERRANEAN FEVER]
None	rs9786232 (G;G)
			[haplogroup:R1]
			[haplogroup:?]
None	rs28936699 (C;C)

			[omim:NON-HODGKIN LYMPHOMA, SOMATIC]
None	rs28941476 (C;C)

			[omim:GRANULOMATOUS DISEASE, CHRONIC, AUTOSOMAL RECESSIVE, CYTOCHROME b-NEGATIVE]
None	rs28933674 (C;C)

			[omim:HEMOPHILIA A]
None	rs28940581 (C;C)

			[omim:FAMILIAL MEDITERRANEAN FEVER]
None	rs28937876 (C;C)

			[omim:POLYCYSTIC LIPOMEMBRANOUS OSTEODYSPLASIA WITH SCLEROSING LEUKOENCEPHALOPATHY]
None	rs28936703 (G;G)

			[omim:SEPTOOPTIC DYSPLASIA, MILD]
None	rs17222279 (G;G)

			[haplogroup:?]
None	rs28934002 (C;C)

			[omim:ALTERNATING HEMIPLEGIA OF CHILDHOOD]
None	rs28933687 (G;G)

			[omim:RETINITIS PIGMENTOSA 2, X-LINKED]
None	rs28940309 (T;T)

			[omim:TRANSPOSITION OF THE GREAT ARTERIES, DEXTRO-LOOPED]
None	rs28936669 (T;T)

			[omim:PSEUDOACHONDROAPLASIA]
None	rs28937585 (T;T)

			[omim:LARSEN SYNDROME, AUTOSOMAL DOMINANT]
None	rs420259 (C;T)	2x risk

			Linked to bipolar disorder in one of the most comprehensive studies to date (2007). Risk allele with reference to dbSNP orientation is reported to be (T), with either one or two copies leading to an odds ratio of 2 (CI 1.6-2.7).
None	rs28936668 (T;T)

			[omim:EPIPHYSEAL DYSPLASIA, MULTIPLE, FAIRBANK TYPE]
None	rs2032589 (D;D)

			[haplogroup:?]
None	rs28933089 (A;A)

			[omim:PACHYONYCHIA CONGENITA, TYPE 2]
None	rs28940298 (C;C)

			[omim:POLYCYTHEMIA, CHUVASH TYPE]
None	rs1800955 (C;C)

			[http://originsgenomeresources.net/musings/?p=119 blog] C allele of rs1800955 DRD4 gene survives an analysis of several dozen studies on genetics and personality. Although small, The evidence from our final meta-analysis indicates that the C-521T may account for up to 3% of phenotypic variance.
None	rs28939719 (T;T)

			[omim:HYPOGONADOTROPIC HYPOGONADISM]
None	rs751229 (A;A)

			13 single-nucleotide polymorphisms (SNPs) in 723 members of 179 Finnish Bipolar disorder families. rs751229(T) and rs3738401(A) was over-transmitted to males with psychotic disorder. under-transmitted rs821616(T) and rs1411771(T) *The risk haplotype for psychotic disorder also associated to perseverations (P = 0.035; for rs751229 alone P = 0.0012), and a protective haplotype G-T-G with rs1655285 in addition to auditory attention (P = 0.0059). [omim:SCHIZOPHRENIA, SUSCEPTIBILITY TO]
None	rs2032650 (C;C)

			[haplogroup:?]
None	rs28934582 (C;C)

			[omim:HYPERURICEMIC NEPHROPATHY, FAMILIAL JUVENILE]
None	rs28937907 (G;G)

			[omim:POLYCYSTIC KIDNEY DISEASE, AUTOSOMAL RECESSIVE]
None	rs17571 (G;G)

			[http://7thspace.com/headlines/279477/cathepsin_d_snp_associated_with_increased_risk_of_variant_creutzfeldt_jakob_disease.html] 110 Variant Creutzfeldt-Jakob disease (vCJD) patients were tested for the C-T base change. significant excess of the cathepsin D polymorphism TT genotype in the vCJD cohort compared to controls. The TT genotype was found to have a 9.75 fold increase in risk of vCJD compared to the CT genotype and a 10.92 fold increase compared to the CC genotype.
None	rs28933371 (T;T)

			[omim:PIEBALDISM]
None	rs28937285 (C;C)

			[omim:HEMOPHILIA A]
None	rs28934578 (C;C)

			[omim:LI-FRAUMENI SYNDROME 1]
None	rs7067418 (G;G)

			[haplogroup:?]
None	rs28933691 (G;G)

			[omim:MENTAL RETARDATION, X-LINKED 45]
None	rs28939720 (C;C)

			[omim:RETINITIS PIGMENTOSA 12]
None	rs28931578 (G;G)

			[omim:APOE2 VARIANT]
None	rs3908 (D;D)

			[haplogroup:?]
None	rs28934592 (G;G)

			[omim:APPARENT MINERALOCORTICOID EXCESS, HYPERTENSION DUE TO]
None	rs28942108 (G;G)

			[omim:NIEMANN-PICK DISEASE, TYPE C1]
None	rs28942099 (G;G)

			[omim:SHWACHMAN-DIAMOND SYNDROME]
None	rs28941773 (C;C)

			[omim:SCAD DEFICIENCY]
None	rs35284970 (C;C)

			[haplogroup:?]
None	rs28937883 (G;G)

			[omim:CONE-ROD DYSTROPHY 9]
None	rs2228479 (G;G)

			rs2228479, known as Val92Met or V92M, is one of several SNPs in the MC1R gene commonly associated with red (or blond) hair and poor tanning, but note it's high presence in one Asian population [PMID 7581459, PMID 16463023] The risk allele is rs2228479(A), compared with the wild-type rs2228479(G) allele. See also [http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=155555&a=155555_AllelicVariant0002 OMIM 155555.0002]
None	rs28937893 (G;G)

			[omim:DEAFNESS, AUTOSOMAL DOMINANT NONSYNDROMIC SENSORINEURAL 6]
None	rs28931579 (A;A)

			[omim:APOE4(+)]
None	rs9786489 (G;G)

			[haplogroup:?]
None	rs28934593 (G;G)

			[omim:APPARENT MINERALOCORTICOID EXCESS, HYPERTENSION DUE TO]
None	rs28939677 (G;G)

			[omim:MULTIPLE EPIPHYSEAL DYSPLASIA, MATN3-RELATED]
None	rs28936688 (G;G)

			[omim:TELANGIECTASIA, HEREDITARY HEMORRHAGIC, TYPE 2]
None	rs28936070 (G;G)

			[omim:CRANIOFRONTONASAL SYNDROME]
None	rs28931569 (A;A)

			[omim:PI M(PROCIDA)]
None	rs28933408 (G;G)

			[omim:THYROID HORMONE RESISTANCE, GENERALIZED, AUTOSOMAL DOMINANT]
None	rs28928881 (G;G)

			[omim:HEMOGLOBIN MALHACEN]
None	rs28942072 (A;A)

			[omim:GM2-GANGLIOSIDOSIS, SUBACUTE]
None	rs28928901 (C;C)

			[omim:EMERY-DREIFUSS MUSCULAR DYSTROPHY, AUTOSOMAL RECESSIVE]
None	rs11570351 (G;G)

			[omim:HIRSCHSPRUNG DISEASE]
None	rs28940875 (C;C)

			[omim:SCAD DEFICIENCY]
None	rs9306848 (C;C)
			[haplogroup:F-R]
			[haplogroup:?]
None	rs28928906 (G;G)

			[omim:CONGENITAL DISORDER OF GLYCOSYLATION, TYPE Ib]
None	rs28933389 (G;G)

			[omim:BCHE, FLUORIDE 1]
None	rs11554495 (C;C)

			[omim:CIRRHOSIS, CRYPTOGENIC]
None	rs28931609 (G;G)

			[omim:CORTICOSTERONE METHYLOXIDASE TYPE II DEFICIENCY]
None	rs2032640 (C;C)

			[haplogroup:?]
None	rs28929469 (G;G)

			[omim:AT-III ROUEN IV]
None	rs165599 (A;A)

			anxiety-related personality traits, ADHD, schizophrenia part of a three marker haplotype rs737865-rs4680-rs165599 epistasis between SNPs in COMT (rs2097603, Val158Met (rs4680), rs165599) and polymorphisms in other schizophrenia susceptibility genes popular in pubmed is associated with bipolar disorder and influences prefrontal aspects of verbal memory in bipolar patients and healthy controls.
None	rs17250992 (T;T)
			[haplogroup:P]
			[haplogroup:?]
None	rs28937898 (C;C)

			[omim:OPTIC ATROPHY AND CATARACT, AUTOSOMAL DOMINANT]
None	rs13447370 (C;C)

			[haplogroup:?]
None	rs861539 (G;G)

			18067C>T possibly related to non-Hodgkin lymphoma rs2040639-AG, contribute to oral cancer risk. pseudo-haplotype with AG-CC genotypes in 2.45x risk rs2040639-rs861539 5.03x risk rs2040639-rs861539-rs2075685 *10.10x risk rs2040639-rs861539-rs2075685-rs1799782
None	rs9341290 (T;T)

			[haplogroup:?]
None	rs6994992 (C;T)

			not conclusive [http://www.jbc.org/cgi/content/abstract/M702953200v1 paper] implicated in schizophrenia effects white matter density and integrity schizophrenia risk-associated The neuregulin 1 promoter polymorphism rs6994992 is not associated with chronic schizophrenia or neurocognition. from snpedia1 by Crowley JJ, Keefe RS, Perkins DO, Stroup TS, Lieberman JA, Sullivan PF Related Articles rs6994992 is '''not''' associated with chronic schizophrenia in a study of 738 patients
None	rs28934576 (C;C)

			[omim:LI-FRAUMENI SYNDROME]
None	rs28933405 (C;C)

			[omim:CARDIOMYOPATHY, FAMILIAL HYPERTROPHIC, 9]
None	rs28940895 (G;G)

			[omim:METACHROMATIC LEUKODYSTROPHY, ADULT]
None	rs28933988 (C;C)

			[omim:SPHEROCYTOSIS, HEREDITARY, JAPANESE TYPE]
None	rs1137100 (G;G)

			affects glucose tolerance and insulin response [omim:LEPTIN RECEPTOR POLYMORPHISM]
None	rs17221964 (T;T)

			[haplogroup:?]
None	rs28933401 (G;G)

			[omim:MIGRAINE, FAMILIAL HEMIPLEGIC, 2]
None	rs16980610 (G;G)

			[haplogroup:?]
None	rs2435357 (C;C)

			This SNP, located in the first intron of the RET gene, has been associated with Hirschsprung disease. The risk allele (in dbSNP orientation) is rs2435357(A), with greater affect in males.
None	rs28940876 (C;C)

			[omim:ALBINISM, OCULOCUTANEOUS, TYPE IA]
None	rs28936371 (G;G)

			[omim:HYPERINSULINEMIC HYPOGLYCEMIA, FAMILIAL, 1]
None	rs28937905 (C;C)

			[omim:MUSCULAR DYSTROPHY, LIMB-GIRDLE, 2I]
None	rs28936395 (G;G)

			[omim:PROSTATE CANCER, PROGRESSION AND METASTASIS OF]
None	rs28928904 (A;A)

			[omim:LONG QT SYNDROME 2]
None	rs9341275 (C;C)

			[haplogroup:?]
None	rs29001584 (A;A)

			[omim:AMYOTROPHIC LATERAL SCLEROSIS 4, JUVENILE]
None	rs28933677 (G;G)

			[omim:HEMOPHILIA A]
None	rs28937578 (C;C)

			[omim:COLORECTAL CANCER]
None	rs28937316 (C;C)

			[omim:LONG QT SYNDROME 3]
None	rs28936696 (A;A)

			[omim:SMALL PATELLA SYNDROME]
None	rs3212236 (A;G)	normal risk

			The more common allele of rs3212236 has been linked to increased risk for developmental dyslexia in a study of ~300 British families. While odds ratios were not reported, the significance was reported as p=0.02.
None	rs28942091 (C;C)

			[omim:ATRIOVENTRICULAR SEPTAL DEFECT, SUSCEPTIBILITY TO, 2]
None	rs28933082 (C;C)

			[omim:SYNPOLYDACTYLY 1]
None	rs28936701 (G;G)

			[omim:GLAUCOMA 3, PRIMARY CONGENITAL, A]
None	rs28936407 (G;G)

			[omim:COLON CANCER, SOMATIC]
None	rs28940574 (C;C)

			[omim:CANAVAN DISEASE]
None	rs28940583 (C;C)

			[omim:SIALIDOSIS, TYPE I]
None	rs16980394 (G;G)

			[haplogroup:?]
None	rs28940573 (G;G)

			[omim:CEROID LIPOFUSCINOSIS, NEURONAL, 2]
None	rs2032681 (I;I)

			[haplogroup:?]
None	rs2306536 (C;C)	average

			rs2306536, a SNP in the CHFR gene, was found to be significantly associated with a lower risk of colorectal cancer (odd ratio 0.53, CI: 0.30-0.94), and to be significantly correlated with the absence of distant metastases, in a case/control study of ~500 Korean patients.
None	rs17315758 (G;G)
			[haplogroup:P]
			[haplogroup:?]
None	rs28928882 (C;C)

			[omim:HEMOGLOBIN GOUDA]
None	rs28933391 (G;G)

			[omim:PYRUVATE DEHYDROGENASE E1-BETA DEFICIENCY]
None	rs28937571 (T;T)

			[omim:PERIODONTITIS, AGGRESSIVE, 1]
None	rs28933985 (C;C)

			[omim:HYPERPROINSULINEMIA, FAMILIAL]
None	rs28937900 (C;C)

			[omim:MUSCULAR DYSTROPHY, LIMB-GIRDLE, 2I]
None	rs7067532 (T;T)

			[haplogroup:?]
None	rs28937272 (T;T)

			[omim:HEMOPHILIA A]
None	rs17222419 (T;T)
			[haplogroup:P]
			[haplogroup:?]
None	rs2032633 (-;-)

			[haplogroup:?]
None	rs28942078 (G;G)

			[omim:FH AFRIKANER 2]
None	rs28931577 (G;G)

			[omim:APOE3 VARIANT]
None	rs28937312 (A;A)

			[omim:THYROXINE-BINDING GLOBULIN DEFICIENCY, COMPLETE]
None	rs28931613 (C;C)

			[omim:MITOCHONDRIAL NEUROGASTROINTESTINAL ENCEPHALOMYOPATHY SYNDROME]
None	rs28931568 (C;C)

			[omim:PI M(MINERAL SPRINGS)]
None	rs28399504 (A;A)

			rs28399504 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*4 variant. This variant has been linked to poor metabolism of compounds like mephenytoin. The risk allele is rs28399504(G). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (Prevacid). [omim:MEPHENYTOIN, POOR METABOLISM OF]
None	rs28934596 (T;T)

			[omim:HEMOCHROMATOSIS]
None	rs28933690 (T;T)

			[omim:MCLEOD SYNDROME]
None	rs28934604 (C;C)

			[omim:VITAMIN D-DEPENDENT RICKETS, TYPE I]
None	rs1558843 (A;A)
			[haplogroup:R]
			[haplogroup:?]
None	rs28933392 (G;G)

			[omim:SEVERE COMBINED IMMUNODEFICIENCY, B CELL-NEGATIVE]
None	rs5030655 (I;I)

			The (-) form of this SNP, representing a deletion of one nucleotide, causes a frameshift such that the resulting CYP2D6 protein is nonfunctional. The associated allele is also known as CYP2D6*6, and there are several subtypes but they are all nonfunctional. If two copies of this (or similar) changes are inherited, CYP2D6 poor metabolism ('PM') is observed. CYP2D6 poor metabolism may affect the efficacy or degree of side effects of drugs metabolized by CYP2D6, such as dextromorphan, sparteine, nortriptyline, venlafaxine and codeine.
None	rs2075181 (G;G)

			[haplogroup:?]
None	rs4762 (G;G)	(?)normal risk

			rs4762, a SNP in the angiotensin II AGT gene, has been reported to be associated with increased risk for developing pre-eclampsia, based on a study of ~180 French-Canadian women. The odds ratio associated with the rs4762(T) allele (encoding methionine) was 1.9 (CI:1.22.9, p=0.0033). Note that rs4762 is commonly referred to in the literature as 'T174M' or 'Thr174Met'; however, databases now indicate that the amino acid that varies is #207 (not 174), as the protein is currently numbered. rs4762 was also reported to play the major role in the 2.1 fold increased risk (CI: 1.4-3.4, p=0.0008) for pre-eclampsia of the rs3889728(A)-rs4762(T)-rs699(C) haplotype.
None	rs28934872 (G;G)

			[omim:TUBEROUS SCLEROSIS 2]
None	rs28929488 (C;C)

			[omim:CORTICOSTEROID-BINDING GLOBULIN DEFICIENCY]
None	rs28940881 (A;A)

			[omim:ALBINISM, OCULAR, AUTOSOMAL RECESSIVE]
None	rs2032626 (A;A)

			[haplogroup:?]
None	rs29001571 (G;G)

			[omim:NEURONOPATHY, DISTAL HEREDITARY MOTOR, TYPE IIB]
None	rs28942092 (C;C)

			[omim:ATRIOVENTRICULAR SEPTAL DEFECT, SUSCEPTIBILITY TO, 2]
None	rs28937598 (G;G)

			[omim:CARDIOENCEPHALOMYOPATHY, FATAL INFANTILE, DUE TO CYTOCHROME c OXIDASE DEFICIENCY]
None	rs28935499 (C;C)

			[omim:FACTOR VIII (OKAYAMA)]
None	rs28937586 (C;C)

			[omim:ATELOSTEOGENESIS, TYPE I]
None	rs28936695 (A;A)

			[omim:MEESMANN CORNEAL DYSTROPHY]
None	rs28937314 (T;T)

			[omim:TANGIER DISEASE]
None	rs28935170 (G;G)

			[omim:CRANIOFRONTONASAL SYNDROME]
None	rs8179021 (C;C)

			[haplogroup:?]
None	rs13266634 (C;T)	increased risk for type-2 diabetes

			rs13266634 is a SNP in the zinc transporter protein member 8 SLC30A8 gene that has primarily been associated with type-2 diabetes in several studies. This SNP is also known as the Arg325Trp or R325W variant; the (C) allele encodes the arginine (R), and the (T) allele encodes the tryptophan (W). significantly associated p = 0.0073; in 1,630 Japanese subjects with type-2 diabetes and in 1,064 controls The major alleles of the SLC30A8 SNP rs13266634 and the HHEX SNP rs7923837 associate with reduced insulin secretion, but not with insulin resistance. 46% of European non-diabetic offspring of type-2 diabetes patients are rs13266634(C;C) homozygotes; they are diabetes-prone and characterised by a 19% decrease in first-phase insulin release following an intravenous glucose load. * Note: this S...
None	rs2073658 (C;C)

			rs2073658 a borderline association with metabolic syndrome was observed (p = 0.036, IDF), the minor allele being the risk-increasing allele. The minor allele of rs2073658 also associated with higher total and LDL-cholesterol, apolipoprotein B-100 and lipoprotein(a) concentrations in longitudinal analyses. rs2073658 is associated with a modestly increased risk to develop type 2 diabetes in Dutch Caucasians, with considerable impact at the population level. [omim:HYPERLIPIDEMIA, FAMILIAL COMBINED, SUSCEPTIBILITY TO]
None	rs28936675 (C;C)

			[omim:HOLOPROSENCEPHALY 3]
None	rs28934873 (A;A)

			[omim:LI-FRAUMENI SYNDROME 1]
None	rs28936676 (A;A)

			[omim:VARIEGATE PORPHYRIA, HOMOZYGOUS]
None	rs28928902 (C;C)

			[omim:MANDIBULOACRAL DYSPLASIA WITH TYPE A LIPODYSTROPHY]
None	rs28942070 (A;A)

			[omim:FRIEDREICH ATAXIA]
None	rs28934602 (A;A)

			[omim:HOLOCARBOXYLASE SYNTHETASE DEFICIENCY]
None	rs917759 (C;C)

			[haplogroup:?]
None	rs28933682 (T;T)

			[omim:HEMOPHILIA A]
None	rs28933406 (G;G)

			[omim:THYROID CARCINOMA, FOLLICULAR, SOMATIC]
None	rs28937875 (C;C)

			[omim:BARDET-BIEDL SYNDROME 6]
None	rs2740981 (A;A)
			[haplogroup:P]
			[haplogroup:?]
None	rs16980499 (T;T)
			[haplogroup:F-R]
			[haplogroup:?]
None	rs2298566 (A;A)	normal

			rs2298566 is a SNP in the MYH15 gene. The risk allele in terms of heart disease is rs2298566(C). This SNP is one of the 5 used by Celera's genetic risk score (GRS) for coronary heart disease (CHD). rs20455, in the KIF6 gene rs3900940, in the MYH15 gene rs7439293, in the PALLD gene rs2298566, in the SNX19 gene *rs1010, in the VAMP8 gene For each of the five variants, the GRS was increased by 1 if the subject was homozygous for the risk variant, unchanged if heterozygous, and decreased by 1 if the individual did not carry the variant. Therefore, individuals carrying all 10 possible risk variants (two copies of each of the five SNPs) were assigned a GRS of 5 and those carrying no risk variants a GRS of -5. A high GRS was defined as 3 or higher. Approximately 4% of the white cohort in ARIC...
None	rs28934906 (G;G)

			[omim:RETT SYNDROME]
None	rs28929471 (C;C)

			[omim:PI P(ST. ALBANS)]
None	rs28936399 (T;T)

			[omim:TELANGIECTASIA, HEREDITARY HEMORRHAGIC, TYPE 2]
None	rs5186 (A;A)	normal risk

			rs5186 is a SNP known as +1166A/C, located in the 3' untranslated region of the angiotensin II receptor type 1 gene AGTR1, which is also known as AT2R1 or AT1R. It is among the most studied of over 50 SNPs in AGTR1. The rs5186(C) allele is associated with increased risk for essential hypertension in Caucasian populations with an odds ratio of 7.3 (homozygote (C;C) compared to (A;C) and (A;A), CI: 1.9-31.9,p=0.0015).[PMID 8021009, PMID 9084931] There are likely to be ethnic differences in risk; while the rs5186(C) allele was associated with hypertension in a Chinese population , it was not been observed as a risk in a Japanese population. Age and gender may also influence risk, as discussed in a review of AGTR1 SNPs and their role in hypertension and related disorders. Pregnant women who ar...
None	rs44707 (T;T)

			rs44707, a SNP in the ADAM33 gene, has been linked to a predisposition to asthma and bronchial hyperresponsiveness. [PMID 12110844, PMID 14564349]
None	rs4804803 (A;G)	some resistance to tuberculosis

			In a study of several African populations, the (G) allele of rs4804803, a SNP in the CD209 gene, was associated with lowered risk of contracting tuberculosis. The odds ratio was 0.75 (CI: 0.61-0.94, p=0.006). The same allele was also associated with less severe medical consequences for those who did contract tuberculosis.
None	rs28937896 (T;T)

			[omim:FAMILIAL COLD AUTOINFLAMMATORY SYNDROME]
None	rs29001665 (G;G)

			[omim:ATAXIA-OCULAR APRAXIA 2]
None	rs28937873 (G;G)

			[omim:ENHANCED S-CONE SYNDROME]
None	rs28940877 (-;-)

			[omim:ALBINISM, OCULOCUTANEOUS, TYPE IA]
None	rs28939087 (C;C)

			[omim:CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIc]
None	rs28928905 (C;C)

			[omim:LONG QT SYNDROME, BRADYCARDIA-INDUCED]
None	rs28935468 (G;G)

			[omim:RETT SYNDROME]
None	rs16981297 (G;G)

			[haplogroup:?]
None	rs17215437 (C;C)

			[omim:HYPOKALEMIC PERIODIC PARALYSIS]
None	rs28933970 (T;T)

			[omim:TOOTH AGENESIS, SELECTIVE, 3]
None	rs28940570 (C;C)

			[omim:BEST MACULAR DYSTROPHY]
None	rs28938172 (T;T)

			[omim:PARKINSON DISEASE 7, AUTOSOMAL RECESSIVE EARLY-ONSET]
None	rs28933385 (G;G)

			[omim:CREUTZFELDT-JAKOB DISEASE]
None	rs28934579 (A;A)

			[omim:SEGAWA SYNDROME, AUTOSOMAL RECESSIVE]
None	rs28930076 (G;G)

			[omim:MARFAN SYNDROME]
None	rs28936672 (C;C)

			[omim:CHOREA, BENIGN HEREDITARY]
None	rs28934568 (T;T)

			[omim:MARFAN SYNDROME, TYPE II]
None	rs28928894 (A;A)

			[omim:PACHYONYCHIA CONGENITA, TYPE 1]
None	rs17222814 (G;G)

			rs17222814, also known as SG13S25, is an ALOX5AP gene SNP that has been defined as part of a haplotype potentially associated with risk for myocardial infarction or ischemic stroke. Details of this haplotype and several related studies are on the ALOX5AP page.
None	rs28940869 (G;G)

			[omim:MUSCLE-EYE-BRAIN DISEASE]
None	rs2196155 (A;A)

			[haplogroup:?]
None	rs3865828 (T;T)
			[haplogroup:P]
			[haplogroup:?]
None	rs28933699 (C;C)

			[omim:PSEUDOACHONDROPLASIA]
None	rs28939707 (A;A)

			[omim:ATELOSTEOGENESIS, TYPE I]
None	rs4141564 (G;G)
			[haplogroup:P]
			[haplogroup:?]
None	rs28933375 (T;T)

			[omim:HEMOPHAGOCYTIC LYMPHOHISTIOCYTOSIS, FAMILIAL, 2]
None	rs28928889 (C;C)

			[omim:HEMOGLOBIN ANAMOSA]
None	rs34442126 (T;T)

			[haplogroup:?]
None	rs28934907 (G;G)

			[omim:RETT SYNDROME]
None	rs28933088 (A;A)

			[omim:PACHYONYCHIA CONGENITA, TYPE 2]
None	rs1802710 (T;T)

			linked to brain tumors and lymphomas popular in pubmed
None	rs28933696 (G;G)

			[omim:CEREBRAL ARTERIOPATHY, AUTOSOMAL DOMINANT, WITH SUBCORTICAL INFARCTS AND LEUKOENCEPHALOPATHY]
None	rs28999110 (G;G)

			[omim:MYASTHENIC SYNDROME, SLOW-CHANNEL CONGENITAL]
None	rs28937592 (C;C)

			[omim:PARKINSON DISEASE]
None	rs28936683 (A;A)

			[omim:FIBULAR HYPOPLASIA AND COMPLEX BRACHYDACTYLY]
None	rs9268428 (G;G)

			Source [http://www.nature.com/ng/journal/v38/n10/fig_tab/ng1885_T1.html nature] multiple sclerosis rs9268428(C) + rs6457594(A) + rs7451962(C)
None	rs1801200 (A;A)

			[omim:ERBB2 POLYMORPHISM]
None	rs9306845 (A;A)
			[haplogroup:F-R]
			[haplogroup:?]
None	rs13447376 (C;C)

			[haplogroup:?]
None	rs28930068 (C;C)

			[omim:HYPOKALEMIC PERIODIC PARALYSIS]
None	rs28940279 (A;A)

			[omim:CANAVAN DISEASE]
None	rs28940878 (A;A)

			[omim:ALBINISM, OCULOCUTANEOUS, TYPE IA]
None	rs28934892 (G;G)

			[omim:THROMBOSIS, HYPERHOMOCYSTEINEMIC]
None	rs28362286 (C;C)

			[omim:LOW DENSITY LIPOPROTEIN CHOLESTEROL, LOW PLASMA LEVELS OF]
None	rs17307656 (G;G)
			[haplogroup:P]
			[haplogroup:?]
None	rs28934584 (C;C)

			[omim:MEDULLARY CYSTIC KIDNEY DISEASE 2]
None	rs28942098 (G;G)

			[omim:HYPERPARATHYROIDISM-JAW TUMOR SYNDROME]
None	rs28934587 (T;T)

			[omim:BARDET-BIEDL SYNDROME 1]
None	rs28933407 (C;C)

			[omim:BURKITT LYMPHOMA]
None	rs28931588 (G;G)

			[omim:PILOMATRICOMA, SOMATIC]
None	rs28936681 (A;A)

			[omim:DYSCHROMATOSIS SYMMETRICA HEREDITARIA]
None	rs9786025 (G;G)

			[haplogroup:?]
None	rs28933074 (T;T)

			[omim:HYPOGONADOTROPIC HYPOGONADISM]
None	rs28935496 (C;C)

			[omim:DIABETES INSIPIDUS, NEPHROGENIC, X-LINKED]
None	rs28939698 (C;C)

			[omim:SMITH-LEMLI-OPITZ SYNDROME]
None	rs28931586 (T;T)

			[omim:IMMUNODEFICIENCY WITH HYPER-IgM, TYPE 3]
None	rs28940872 (C;C)

			[omim:SCAD DEFICIENCY]
None	rs17316597 (G;G)

			[haplogroup:?]
None	rs10871777 (A;A)	normal

			See rs17782313 for details.
None	rs28942105 (T;T)

			[omim:NIEMANN-PICK DISEASE, TYPE C1]
None	rs28935471 (T;T)

			[omim:FRONTOMETAPHYSEAL DYSPLASIA]
None	rs28939702 (G;G)

			[omim:PSEUDOXANTHOMA ELASTICUM]
None	rs28940882 (C;C)

			[omim:GALACTOSE EPIMERASE DEFICIENCY]
None	rs28933683 (G;G)

			[omim:MASA SYNDROME]
None	rs28933672 (C;C)

			[omim:HEMOPHILIA A]
None	rs28933092 (A;A)

			[omim:CARDIOMYOPATHY, DILATED, 1A]
None	rs3970559 (G;G)

			[omim:HYPERPROLINEMIA, TYPE I]
None	rs28937877 (T;T)

			[omim:MACULAR CORNEAL DYSTROPHY, TYPE I]
None	rs2269648 (C;T)

			[http://genetics.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pgen.0030120.eor linked] to Cardiovascular Events Several CVD risk variants were identified: In women, the combination of F5 rs7542281 THBD rs1042580, together with three single F5 SNPs, was associated with CVD events. Among men, PROC rs1041296, when combined with either ICAM1 rs5030341 or F5 rs2269648, was associated with total mortality. As a single variant, PROC rs1401296, together with the F5 Leiden mutation, was associated with ischemic stroke events.
None	rs9785717 (A;A)
			[haplogroup:R1]
			[haplogroup:?]
None	rs28933692 (C;C)

			[omim:HIGH DENSITY LIPOPROTEIN DEFICIENCY]
None	rs28939692 (G;G)

			[omim:NAIL-PATELLA SYNDROME]
None	rs28933669 (A;A)

			[omim:HEMOPHILIA A]
None	rs28937892 (C;C)

			[omim:WOLFRAM SYNDROME]
None	rs28936685 (T;T)

			[omim:RIPPLING MUSCLE DISEASE 2]
None	rs28936379 (A;A)

			[omim:ALZHEIMER DISEASE, FAMILIAL, 4]
None	rs28937595 (C;C)

			[omim:THIAMINE-RESPONSIVE MEGALOBLASTIC ANEMIA SYNDROME]
None	rs28934876 (T;T)

			[omim:CONGENITAL DISORDER OF GLYCOSYLATION, TYPE Ij]
None	rs3087456 (A;A)

			This snp has been linked to increased risk of [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16849401&query_hl=3&itool=pubmed_docsum adrenal insufficiency] however there is mixed information regarding several other autoimmune diseases in a german population [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16426246&query_hl=10&itool=pubmed_docsum] Promoter polymorphism rs3087456 in the MHC class II transactivator gene is not associated with susceptibility for selected autoimmune diseases in German patient groups. [omim:RHEUMATOID ARTHRITIS, SUSCEPTIBILITY TO]
None	rs28934610 (G;G)

			[omim:USHER SYNDROME, TYPE IB]
None	rs28936388 (C;C)

			[omim:GITELMAN SYNDROME]
None	rs28932769 (A;A)

			[omim:ALEXANDER DISEASE]
None	rs28935472 (C;C)

			[omim:MELNICK-NEEDLES SYNDROME]
None	rs28942090 (A;A)

			[omim:CONGENITAL DISORDER OF GLYCOSYLATION, TYPE Ig]
None	rs10488631 (-;-)

			Systemic Lupus Erythematosus rs10488631 rs2004640 rs10954213 and rs729302
None	rs8179022 (G;G)

			[haplogroup:?]
None	rs9786781 (A;G)

			[haplogroup:?]
None	rs28931610 (C;C)

			[omim:SKIN FRAGILITY-WOOLLY HAIR SYNDROME]
None	rs28936368 (G;G)

			[omim:EPIPHYSEAL DYSPLASIA, MULTIPLE, FAIRBANK TYPE]
None	rs28936401 (C;C)

			[omim:TELANGIECTASIA, HEREDITARY HEMORRHAGIC, TYPE 2]
None	rs2412522 (-;-)

			risk of cardiovascular disease rs2412522 for mean corpuscular hemoglobin concentration was 7*10(-8)
None	rs28935483 (A;A)

			[omim:GLYCEROL KINASE DEFICIENCY, ISOLATED]
None	rs28935171 (C;C)

			[omim:COFFIN-LOWRY SYNDROME]
None	rs574174 (C;C)

			rs574174, a SNP in the ADAM33 gene, has been linked to a predisposition to asthma and bronchial hyperresponsiveness. [PMID 12110844, PMID 14564349]
None	rs28931596 (T;T)

			[omim:OCULODENTODIGITAL DYSPLASIA]
None	rs28933670 (A;A)

			[omim:HEMOPHILIA A]
None	rs28933374 (G;G)

			[omim:HEMOPHAGOCYTIC LYMPHOHISTIOCYTOSIS, FAMILIAL, 2]
None	rs28934598 (C;C)

			[omim:GLYCINE ENCEPHALOPATHY]
None	rs9785905 (A;A)
			[haplogroup:F-R]
			[haplogroup:?]
None	rs28933681 (C;C)

			[omim:HEMOPHILIA A]
None	rs28937583 (T;T)

			[omim:ERYTHROKERATODERMIA VARIABILIS, AUTOSOMAL RECESSIVE]
None	rs28936403 (C;C)

			[omim:HOLOPROSENCEPHALY 7]
None	rs28931615 (C;C)

			[omim:CROUZON SYNDROME WITH ACANTHOSIS NIGRICANS]
None	rs28933388 (C;C)

			[omim:LEUKEMIA, JUVENILE MYELOMONOCYTIC]
None	rs28934594 (C;C)

			[omim:APPARENT MINERALOCORTICOID EXCESS, HYPERTENSION DUE TO]
None	rs28942069 (G;G)

			[omim:FRIEDREICH ATAXIA]
None	rs28942079 (G;G)

			[omim:FH ALGERIA]
None	rs16980370 (A;A)

			[haplogroup:?]
None	rs16981290 (C;C)

			[haplogroup:?]
None	rs28935769 (T;T)

			[omim:PYRUVATE DEHYDROGENASE E1-BETA DEFICIENCY]
None	rs28933080 (A;A)

			[omim:HEMOGLOBIN F (CALABRIA)]
None	rs28928873 (C;C)

			[omim:HYPERINSULINEMIC HYPOGLYCEMIA, FAMILIAL, 6]
None	rs28940280 (G;G)

			[omim:CEROID LIPOFUSCINOSIS, NEURONAL, 5]
None	rs3897 (A;A)

			[haplogroup:?]
None	rs28931604 (G;G)

			[omim:CATARACT, CONGENITAL LAMELLAR]
None	rs28928871 (C;C)

			[omim:OVARIAN HYPERSTIMULATION SYNDROME]
None	rs3905 (T;T)

			[haplogroup:?]
None	rs28940586 (T;T)

			[omim:HEMOCHROMATOSIS, TYPE 2A]
None	rs8179176 (C;C)

			Among women rs8179176 rs9340799 rs1256065 and rs1256030 were associated with likelihood of developing cognitive impairment. In men, one of the rs728524 rs1255998 rs1256030 were associated with cognitive impairment.
None	rs28937594 (A;A)

			[omim:INCLUSION BODY MYOPATHY, AUTOSOMAL RECESSIVE]
None	rs28931612 (C;C)

			[omim:PARATHYROID ADENOMA, SOMATIC]
None	rs28934575 (C;C)

			[omim:OSTEOSARCOMA]
None	rs2068150 (C;C)

			[haplogroup:?]
None	rs28929495 (G;G)

			[omim:NONSMALL CELL LUNG CANCER, RESPONSE TO TYROSINE KINASE INHIBITOR IN, SOMATIC]
None	rs28939077 (A;A)

			[omim:TRIGLYCERIDE STORAGE DISEASE WITH IMPAIRED LONG-CHAIN FATTY ACID]
None	rs28937579 (T;T)

			[omim:HYPERCHOLANEMIA, FAMILIAL]
None	rs28931603 (G;G)

			[omim:COPROPORPHYRIA]
None	rs28939681 (G;G)

			[omim:CHARCOT-MARIE-TOOTH DISEASE, AXONAL, TYPE 2F]
None	rs28934891 (C;C)

			[omim:HOMOCYSTINURIA, PYRIDOXINE-RESPONSIVE]
None	rs20321 (G;G)

			[haplogroup:?]
None	rs3895 (T;T)

			[haplogroup:?]
None	rs28933077 (A;A)

			[omim:HEMOGLOBIN A(2) SANT' ANTIOCO]
None	rs28937286 (C;C)

			[omim:HEMOPHILIA A]
None	rs28931595 (C;C)

			[omim:DEAFNESS, AUTOSOMAL DOMINANT NONSYNDROMIC SENSORINEURAL 3]
None	rs2032647 (A;A)
			[haplogroup:BR]
			[haplogroup:?]
None	rs17860424 (C;C)

			[omim:CASPASE 8 DEFICIENCY]
None	rs28936686 (G;G)

			[omim:RIPPLING MUSCLE DISEASE 2, AUTOSOMAL RECESSIVE]
None	rs28937581 (G;G)

			[omim:MIYOSHI MYOPATHY]
None	rs6277 (G;G)	(?)1.6x higher schizophrenia risk

			rs6277 is one of several SNPs in the dopamine receptor DRD2 gene. In a study of 300+ Russian patients with schizophrenia, the rs6277(C) allele was associated with higher risk. From a pooled meta-study (total of 4 other reports plus this one) the allelic odds ratio is 1.42 (CI: 1.26-1.61, p<0.00005), and the genotypic odds ratio for the (C;C) genotype was 1.6 (CI: 1.32-1.95, p<0.00005). Note that rs6275 and rs6277 are only 18bp apart, hence their very tight linkage (r²=1).
None	rs2032679 (T;T)

			[haplogroup:?]
None	rs28935202 (G;G)

			[omim:HEMOPHILIA A]
None	rs28935475 (G;G)

			[omim:2-@METHYL-3-HYDROXYBUTYRYL-CoA DEHYDROGENASE DEFICIENCY]
None	rs34289137 (C;C)

			[haplogroup:?]
None	rs28928891 (A;A)

			[omim:BRACHYDACTYLY, TYPE E]
None	rs28940315 (C;C)

			[omim:LEBER CONGENITAL AMAUROSIS, TYPE III]
None	rs28999111 (G;G)

			[omim:DEAFNESS, AUTOSOMAL DOMINANT 20]
None	rs28940588 (C;C)

			[omim:CONGENITAL DISORDER OF GLYCOSYLATION, TYPE Id]
None	rs17316592 (T;T)

			[haplogroup:?]
None	rs1799768 (D;D)

			This SNP is equivalent to, and therefore please go to, rs1799889 for related information.
None	rs28942106 (T;T)

			[omim:NIEMANN-PICK DISEASE, TYPE C1, JUVENILE FORM]
None	rs28933972 (C;C)

			[omim:TOOTH AGENESIS, SELECTIVE, 3]
None	rs9786893 (C;C)

			[haplogroup:?]
None	rs2032677 (T;T)

			[haplogroup:?]
None	rs28939091 (A;A)

			[omim:USHER SYNDROME, TYPE III]
None	rs28929480 (C;C)

			[omim:SPHEROCYTOSIS, HEREDITARY, DUE TO BAND 3 CAPE TOWN]
None	rs28357980 (G;G)
			also known as is a mitochondrial snp 4917G [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0002091 PLoS] this snp predicts the presence of age related macular degeneration (OR = 2.16, 95%CI 1.203.91, p = 0.01). This genotype is likely to have many other effects
			also known as is a mitochondrial snp 4917G [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0002091 PLoS] this snp predicts the presence of age related macular degeneration (OR = 2.16, 95%CI 1.203.91, p = 0.01). [http://www.thinkgene.com/cells-power-plant-genes-raise-vision-disorder-risk/ ThinkGene] coverage
None	rs28933694 (A;A)

			[omim:MUSCULAR DYSTROPHY, LIMB-GIRDLE, TYPE 2D]
None	rs28933990 (G;G)

			[omim:BOTHNIA RETINAL DYSTROPHY]
None	rs28940874 (C;C)

			[omim:SCAD DEFICIENCY]
None	rs2032671 (C;C)

			[haplogroup:?]
None	rs11575897 (G;G)

			[haplogroup:?]
None	rs28931594 (C;C)

			[omim:KERATITIS-ICHTHYOSIS-DEAFNESS SYNDROME]
None	rs2032629 (G;G)

			[haplogroup:?]
None	rs28933697 (G;G)

			[omim:CEREBRAL ARTERIOPATHY, AUTOSOMAL DOMINANT, WITH SUBCORTICAL INFARCTS AND LEUKOENCEPHALOPATHY]
None	rs28934905 (A;A)

			[omim:RETT SYNDROME]
None	rs9341310 (C;C)

			[haplogroup:?]
None	rs28940577 (T;T)

			[omim:FAMILIAL MEDITERRANEAN FEVER]
None	rs9786301 (G;G)

			[haplogroup:?]
None	rs28931581 (C;C)

			[omim:ACROMESOMELIC DYSPLASIA, MAROTEAUX TYPE]
None	rs9341313 (T;T)

			[haplogroup:?]
None	rs4994 (A;A)

			[omim:OBESITY, SUSCEPTIBILITY TO]
None	rs28928910 (G;G)

			[omim:CHARCOT-MARIE-TOOTH DISEASE, AXONAL, TYPE 2E]
None	rs1049564 (A;A)

			[omim:NUCLEOSIDE PHOSPHORYLASE POLYMORPHISM]
None	rs28931576 (A;A)

			[omim:APOE3(-)-FREIBURG]
None	rs2032632 (T;T)

			[haplogroup:?]
None	rs28937313 (T;T)

			[omim:TANGIER DISEASE]
None	rs28934572 (C;C)

			[omim:LI-FRAUMENI SYNDROME 1]
None	rs28929768 (A;A)

			[omim:MYASTHENIC SYNDROME, SLOW-CHANNEL CONGENITAL, AUTOSOMAL RECESSIVE]
None	rs28933668 (G;G)

			[omim:HEMOPHILIA A]
None	rs28937874 (A;A)

			[omim:EPILEPSY, LATERAL TEMPORAL LOBE, AUTOSOMAL DOMINANT]
None	rs28937573 (C;C)

			[omim:CATARACT, MARNER TYPE]
None	rs2032594 (T;T)

			[haplogroup:?]
None	rs28937568 (C;C)

			[omim:NEURONOPATHY, DISTAL HEREDITARY MOTOR, TYPE IIB]
None	rs28939715 (C;C)

			[omim:NEUROBLASTOMA]

Ambiguous
0.0	rs1800435 (C;C) ambig

			[omim:AMINOLEVULINATE DEHYDRATASE, ALAD1/ALAD2 POLYMORPHISM]
0.0	rs7775 (G;G) ambig

			rs7775 (R324G) osteoarthritis at multiple joints (p = 0.07), particularly in the hip in women associated with osteoarthritis of the hip in females This is an arg324-to-gly (R324G) substitution [omim:OSTEOARTHRITIS OF HIP, FEMALE-SPECIFIC, SUSCEPTIBILITY TO]
0.0	rs28997576 (C;C) ambig

			[omim:BREAST CANCER, SUSCEPTIBILITY TO]
0.0	rs28903098 (G;G) ambig

			[omim:BREAST CANCER, EARLY-ONSET]
0.0	rs4253208 (G;G) ambig	possible COCKAYNE SYNDROME, TYPE B

			[omim:COCKAYNE SYNDROME, TYPE B]
0.0	rs12735723 (C;C) ambig

			[omim:VARIEGATE PORPHYRIA, HOMOZYGOUS]
0.0	rs9785940 (C;C) ambig

			[haplogroup:?]
0.0	rs16980363 (C;C) ambig

			[haplogroup:?]
1.7	rs2297404 (C;C) ambig

			rs2297404, rs2230808, and rs2020927 haplotype (CAC) was more prevalent in the Alzheimer's disease group (0.323 in AD vs. 0.202 in control); while haplotype1 (TGG) was over-represented in the healthy controls (0.595 in control vs. 0.493 in AD)
1.7	rs3817964 (T;T) ambig	6x higher risk of RA

			This SNP, along with SNPs rs6910071 and rs660895, is a tag SNP for the HLA-DRB10401 allele. The HLA-DRB10401 allele has been associated with higher risk for rheumatoid arthritis, and in particular, rheumatoid vasculitis. The association is seen particularly for individuals carrying two copies of, i.e. homozygous for, the allele. The reported odds ratio for rs3817964(T;T) homozygotes is 6.2 (CI: 1.01 - 37.9). The risk for rheumatoid arthritis may be higher for individuals carrying one copy (one 'dose') of the HLA-DRB10401 allele, if they also carry a different HLA-DRB1 risk allele. In particular, 0401/0404 individuals are reported to have an odds ratio for rheumatoid vasculitis of 4.1 (CI: 1.1 - 16.2), and 0401/*0101 individuals have an odds ratio of 4.0 (CI: 1.4 - 11.6).
1.7	rs1255998 (G;G) ambig

			Among women rs8179176 rs9340799 rs1256065 and rs1256030 were associated with likelihood of developing cognitive impairment. In men, one of the rs728524 rs1255998 rs1256030 were associated with cognitive impairment.
3.3	rs17222244 (C;C) ambig

			[haplogroup:?]
3.3	rs17315680 (G;G) ambig

			[haplogroup:?]
3.4	rs594242 (G;G) ambig

			Three (rs643627-rs594242-rs6311: A-C-T), two (rs594242-rs6311: C-T) and a single functional (rs6311: T) marker were protective against suicidal behavior. The complementary makers (rs594242-rs6311: G-C and rs6311: C) were associated with increased risk for non-violent and impulsive suicidal behavior. Furthermore, CC-homozygotes for the functional SNP rs6311 reported more anger- and aggression-related behavior.
5.0	rs12026 (G;G) ambig

			reports that one or two copies of a common variation (glycine replacing alanine) present at amino acid 148 of the PON2 protein, rs12026, exacerbates glycemia in non-insulin dependent diabetes mellitus (NIDDM).
11.7	rs2296336 (C;C) ambig	normal

			rs2296336 has been reported in a Swedish study to be associated with type-1 diabetes. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.3 (CI 1.00-1.69), and for homozygotes, 2.9 (CI 1.88-4.59). suggests this snp does not play a role in type-1 diabetes.
18.3	rs2287499 (C;G) ambig

			ER negative breast cancer association rs2287499, OR (95% CI) = 1.08 (0.95-1.23) for CG vs. CC and 1.60 (1.04-2.47) for GG vs. CC, p-trend = 0.01) (OR (95% CI) per variant allele: 1.42 (1.18-1.71) p-trend = 0.00009).
18.6	rs11196205 (C;C) ambig

			rs12255372, rs7903146, rs7901695 and rs11196205 associated with type-2 diabetes
23.3	rs1800795 (G;G) ambig	more IL6; certain risks, see details
			rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. In the literature, it is almost universally referred to as the IL6 '-174' polymorphism. It tends to be quite polymorphic in Caucasians, but Asian and African populations are almost monomorphic (for the (G) allele). The rs1800795(G) allele, generally associated with higher levels of IL6, has been associated with increased risk in the following studies: * The rs1800795(G) allele was significantly associated with type-2 diabetes (odds ratio 1.51, CI: 1.11-2.07, p=0.0096) in a study of 700 elderly Caucasians. * Following a kidney transplant, patients with rs1800795(G;G) genotypes have a higher risk of new-onset diabetes an...
			rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. In the literature, it is almost universally referred to as the IL6 '-174' polymorphism. It tends to be quite polymorphic in Caucasians, but Asian and African populations are almost monomorphic (for the (G) allele). It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. Studies on rs1800795 now include potential associations with heart disease, Kaposi's sarcoma, type-2 diabetes, stroke, obesity, Hodgkin's lymphoma, sudden ...
23.7	rs279845 (T;T) ambig

			This SNP in the GABRA2 gene has been linked to Alcoholism. The strongest association for this SNP is seen when it is a member of a haplotype consisting of the rs279871(A) + rs279845(T) + rs279836(A) alleles .
25.4	rs279836 (T;T) ambig

			This SNP in the GABRA2 gene has been linked to Alcoholism. The strongest association for this SNP is seen when it is a member of a haplotype consisting of the rs279871(A) + rs279845(T) + rs279836(A) alleles .
28.3	rs2293869 (A;A) ambig

			[omim:HYPERTRIGLYCERIDEMIA, SUSCEPTIBILITY TO]
30.0	rs3900 (G;G) ambig
			[haplogroup:K-R]
			[haplogroup:?]
30.0	rs17250887 (A;A) ambig

			[haplogroup:?]
30.0	rs9785959 (G;G) ambig
			[haplogroup:R1]
			[haplogroup:?]
30.0	rs1042714 (C;G) ambig	complex; see details for increased risks

			Several susceptibilities have been linked to rs1042714, a SNP in the ADRB2 gene that is also known as the Q27E SNP. The rs1042714(C) allele encodes the glutamine (Gln; 'Q'), and the rs1042714(G) allele encodes the glutamic acid (Glu; 'E'). A study of 304 patients found that the Glu27 allele led to increased risk for idiopathic venous thromboembolism; the reported odds ratio was 1.40 (CI: 1.09-1.79, p=0.006) for carriers of at least one risk allele. A study of 334 families with at least one child with autism found that increased risk associated with the rs1042714(G;G) homozygous genotype; the odds ratio reported was between 1.33-1.60 (CI: 1.07-2.58). The risk was approximately doubled among mothers who had clinical markers for pregnancy related stress. In a study of 342 patients with type-2...
30.2	rs4950928 (C;G) ambig

			rs4950928 in CHI3L1 is likely to play roles in the predisposition to schizophrenia.
30.5	rs324650 (A;A) ambig	normal. rare for asians.

			Category:interesting This snp (and perhaps its neighbors) may influence intelligence and alcohol dependence and or this [http://www.tweelingenregister.org/nederlands/verslaggeving/congresbezoek/Gosso_ESHG_2006.pdf pdf poster] show association between the CHRM2 gene and intelligence . In this study of ~300 Caucasians, the (T;T) genotype appeared to typically have a 4 point higher IQ than the (A;T) genotype, which had a 4 point higher IQ (on average) than the (A;A) genotype. A nearby SNP, rs324640, showed similar results to rs324650, and was in linkage disequilibrium (r2 = 0.90) with it. CHRM2 gene predisposes to alcohol dependence, drug dependence and affective disorders: results from an extended case-control structured association study. And the earlier
31.7	rs523349 (C;G) ambig	increased ovarian cancer risk

			rs523349 is a SNP in the steroid-5-alpha-reductase SRD5A2 gene; it is also known as V89L. In a study of a total of 1,466 Caucasian cases of ovarian cancer, the rs523349(G) allele showed a significant trend of increasing risk of ovarian cancer per rare allele (p = 0.00002). showed '''no association''' with ovarian cancer risk 4,624 invasive epithelial ovarian cancer cases and 8,113 controls of white non-Hispanic origin ovarian cancer
33.3	rs6318 (G;G) ambig

			[omim:SEROTONIN 5-HT-2C RECEPTOR POLYMORPHISM]
36.7	rs1801253 (C;G) ambig	depends on [[rs1801252]]

			Variation at this SNP, located in the ADRB1 gene, may encode either the amino acid glycine or arginine at amino acid position 389 of the corresponding protein, the beta-1 adrenergic receptor. This protein is the target of beta blocker drugs, and so how well the drug works to help lower a patients high blood pressure depends in part on this SNP. The status of this SNP is often reported together with the status of SNP rs1801252, which encodes an amino acid variant at position 49 of the same (ADRB1) protein. One of the best known studies of the effects of these 2 separate SNPs on the average efficacy of the beta blocker metoprolol in lowering blood pressure (BP) can be summarized for patients with the corresponding genotypes as follows : *rs1801252(A;A) and rs1801253(C;C) carriers: 15 point d...
41.7	rs2301612 (C;C) ambig

			[omim:THROMBOTIC THROMBOCYTOPENIC PURPURA, CONGENITAL]
41.7	rs7566605 (C;G) ambig	?
			This is the genotype of User:Watson
			rs7566605 was initially reported as being associated in at least 4 independent populations as being associated with obesity. [http://www.microarraybulletin.com/community/uploaded_images/WorkflowPDFs/C_H_WFChart.pdf Poster] At least one population has since been reported in which this association was not seen. On the other hand, a report has also been published indicating that obese children who are rs7566605(C;C) homozygotes find it harder to lose weight in clinical intervention programs than (C;G) heterozygotes or (G;G) homozygotes, which supports the association of SNP rs7566605 with obesity.
43.3	rs1801198 (C;G) ambig

			[omim:TCN2 POLYMORPHISM]
43.3	rs380390 (C;G) ambig

			linked to blindness in old age rs3753394, rs800292, rs1061147, rs1061170, rs380390, and rs1329428 CFH variations appear to contribute to ARMD in Caucasians, but not in Japanese
43.3	rs324981 (A;T) ambig

			asthma related influences sleep patterns [http://originsgenomeresources.net/musings/?p=62] [omim:ASTHMA SUSCEPTIBILITY 2]
45.0	rs6887695 (G;G) ambig

			IL12B gene SNP, part of a haplotype with rs3212227 associated with psoriasis.
46.7	rs4918 (C;C) ambig

			Category:is a snp [http://cat.inist.fr/?aModele=afficheN&cpsidt=16815755] Homozygosity for the rs2593813:G-rs4917:Met-rs4918:Ser haplotype conferred an increased risk for leanness
48.3	rs713598 (C;G) ambig	can taste bitter
			This is the genotype of User:Watson
			rs713598 is one of three SNPs that form the main haplotypes behind the ability to perceive as bitter the taste of the compound phenylthiocarbamide (PTC) and similar molecules in foods (like cabbage and raw broccoli) or drinks (like coffee and dark beers). The rs713598(G) allele, in the orientation shown in dbSNP, is the 'tasting' allele, and it is dominant to the 'non-tasting' allele rs713598(C), so having one copy is enough to have the bitter tasting ability. If you are a 'taster', you're also likely to carry at least one rs10246939(C) and one rs1726866(C) allele since, along with rs713598(G), these three SNPs form the most common tasting haplotype. If you lack these alleles, you're quite likely (~80%) to be a non-taster of bitterness, meaning that foods that may taste bitter to others ta...
49.2	rs287235 (C;C) ambig

			The (G) allele of this snp has been implicated in a somewhat increased risk of developing late onset Parkinson's disease
55.0	rs17651507 (A;A) ambig

			This SNP was identified as a 'core' SNP helping to define one (of nine total) runs of homozygosity (ROH) potentially associated with increased risk for schizophrenia. Each region consists of at least 100 consecutive SNPs, generally spanning 500KB or more, for which both chromosomes in an individual were homozygous. The overall odds ratio for schizophrenia associated with inheriting 1, 2, or 3 of these 9 ROHs was calculated to be 3.3, 5.4, or 24, respectively, with 95% confidence intervals of (1.9-5.7), (3.7-16.1), and (6.9-83.9), respectively. This particular SNP, rs17651507, was deemed to be the core SNP of a region on chromosome 17 with 211 SNPs spanning 1453KB from 17:141169023 to 17:42622984 (build 35). Potentially independent of the ROH, the risk allele for this SNP in the orientation...
61.7	rs1042522 (G;G) ambig	(?)longer lifespan?

			This SNP, a variant in the TP53 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (C). The minor allele encodes an arginine at position 72 of the protein (where there's normally a proline), and the SNP is commonly called the Arg72 variant, although P72R is also common in the literature. Minor allele homozygotes, i.e. rs1042522(C;C) genotypes, live on average 3 years longer than major allele (G;G) homozygotes, based on a study of 9,200+ Danish individuals. The increased longevity is speculate...
68.3	rs11739135 (C;G) ambig

			rs11739135 is reported to confer susceptibility to Crohn's disease.
68.3	rs2273535 (A;A) ambig	common

			SNP rs2273535, also known as F31I or Phe31Ile, has been associated with increased risk for several cancers, in most cases when individuals are homozgyous for the risk allele, rs2273535(T), as oriented to the dbSNP entry. A meta-analysis of almost 10,000 cases of breast, colon, ovarian, prostate, lung, esophageal and non-melanoma skin cancer, compared to an equal number of Caucasian controls, determined the following risks (i.e., odds ratios, OR) : For colorectal cancer: OR for homozygotes of 1.5 (CI: 1.14-1.99) For breast cancer: OR for homozygotes of 1.35 (CI: 1.12-1.64) *For any of the cancer types studied: OR for heterozygotes of 1.10 (CI: 1.03-1.18), OR for homozygotes of 1.40 (CI: 1.22-1.59) In a Chinese population, breast cancer risk for rs2273535(T;T) homozygotes compared to the o...
68.3	rs2049045 (G;G) ambig

			Alzheimer's disease risk for non ApoE4 carriers is affected by the heterozygous form of rs6265, as well as the diplotypes of rs6265, rs11030104, and rs2049045.
70.0	rs8181264 (C;C) ambig
			[haplogroup:P]
			[haplogroup:?]
70.0	rs1800437 (G;G) ambig	average

			SNP rs1800437, located in the coding region of the GIPR gene and known as Glu354Gln, shows a marginal association with cardiovascular disease (CVD) in a study of ~200 patients from a Dutch population. Heterozygotes are reported to be at lower risk for CVD, with an odds ratio of 0.72 (CI: 0.52 - 0.97, p=0.03). However, no significant association was seen for homozygous carriers of the minor allele.
70.0	rs17306671 (T;T) ambig

			[haplogroup:?]
70.0	rs4116821 (G;G) ambig
			[haplogroup:P]
			[haplogroup:?]
73.3	rs7732671 (G;G) ambig

			[omim:OBESITY, VARIATION IN]
75.0	rs11053646 (C;C) ambig

			[omim:MYOCARDIAL INFARCTION, SUSCEPTIBILITY TO]
76.7	rs1045485 (G;G) ambig

			also known as D302H [PMID 15601643, PMID 17018785, PMID 17293864] Several large studies indicate that the (C) allele of this SNP, located in exon 10 of the CASP8 gene, may reduce the risk of Breast Cancer in a dose dependent manner [http://www.infozine.com/news/stories/op/storiesView/sid/20982/ article] [http://cancergenetics.wordpress.com/2007/10/05/caspase-8-story-breast-cancer/ cancergenetics] showed '''no association''' with ovarian cancer risk 4,624 invasive epithelial ovarian cancer cases and 8,113 controls of white non-Hispanic origin ovarian cancer
81.7	rs8179183 (G;G) ambig

			[omim:LEPTIN RECEPTOR POLYMORPHISM]
86.7	rs1801282 (C;C) ambig

			The association between type-1 diabetes and SNP rs1801282 is mentioned as being replicated in rs1801282 and risk of cognitive decline in elders? Maybe with diabetes.
86.7	rs1800947 (G;G) ambig

			Although somewhat lacking in statistical power, several reports have linked rs1800947, a synonymous mutation known as CRP2 in the C-reactive protein CRP to the autoimmune disorder SLE, systemic lupus erythematosus. The risk allele in dbSNP orientation is (C). [PMID 14645206, PMID 15897982, PMID 18216863] [omim:C-REACTIVE PROTEIN, PENTRAXIN-RELATED; CRP]
88.3	rs3135506 (G;G) ambig

			no known effect also known as S19W discussed in , however the snp which prevents [http://www.medicalnewstoday.com/medicalnews.php?newsid=67543 weight gain from high fat diets] is rs662799
90.0	rs2250889 (C;C) ambig	1.69x higher risk for lung cancer

			rs2250889, a SNP also known as P574R, is located in the MMP9 gene. In a study of 744 Chinese patients with incident lung cancer rs2250889(C;G) heterozygotes and rs2250889(C;C) homozygotes had 1.46-fold (CI: 0.94-2.26) and 1.69-fold elevated risk (CI: 1.10-2.60) for lung cancer, respectively, compared with the (G;G) genotype. There was an additive effect of having additional MMP9 risk alleles.
91.4	rs1800796 (G;G) ambig

			rs1800796 IL-6 572G>C polymorphism (and h.211 haplotype) is associated with Abdominal Aortic Aneurysm (AAA) [PMID 17508011 Our results provide evidence that there is a clear genetic influence of IL6 -572C>G polymorphism on plasma levels of fibrinogen and CRP, but this polymorphism does not lead to elevated blood pressure. rs1800797, rs1800796 and rs1800795 have been shown to affect both the transcription and secretion of IL-6, to symptomatic distal interphalangeal osteoarthritis based on 535 women. the G alleles of two promoter single-nucleotide polymorphisms (SNP) G-597A and G-174C were more common among the subjects with symptomatic DIP OA than among those with no disease (p-values corrected for multiple testing 0.020 and 0.024). Also, the carriage of at least one G allele in these posi...
96.7	rs17306657 (C;C) ambig

			[haplogroup:?]
96.7	rs2066845 (G;G) ambig

			rs2066845, a SNP in the NOD2 gene, has been linked to Crohn's disease. rs2066845 has also been reported, with an odds ratio of 3.5 (CI 1.517.01), to be associated with psoriatic arthritis. [omim:CROHN DISEASE, SUSCEPTIBILITY TO]
96.7	rs16891982 (G;G) ambig	european

			This snp influences skin pigmentation. The allele p.L374F indicates light-skinned european ancestry
100.0	rs3910 (T;T) ambig

			[haplogroup:?]
100.0	rs2032646 (C;C) ambig

			[haplogroup:?]
100.0	rs9306841 (C;C) ambig
			[haplogroup:E]
			[haplogroup:?]
100.0	rs2032657 (T;T) ambig

			[haplogroup:?]
100.0	rs2032622 (A;A) ambig

			[haplogroup:?]
100.0	rs2032630 (T;T) ambig
			[haplogroup:BR]
			[haplogroup:?]
100.0	rs2032653 (G;G) ambig

			[haplogroup:?]
100.0	rs2032628 (A;A) ambig

			[haplogroup:?]
100.0	rs28989183 (G;G) ambig

			[omim:MOSAIC VARIEGATED ANEUPLOIDY SYNDROME]
100.0	rs9786634 (G;G) ambig

			[haplogroup:?]
100.0	rs4589047 (T;T) ambig
			[haplogroup:F-R]
			[haplogroup:?]
None	rs16980577 (T;T) ambig

			[haplogroup:?]
None	rs28935168 (G;G) ambig

			[omim:RETT SYNDROME]
None	rs1064651 (C;C) ambig

			[omim:GAUCHER DISEASE, TYPE IIIC]
None	rs28937273 (A;A) ambig

			[omim:HEMOPHILIA A]
None	rs28935176 (C;C) ambig

			[omim:AGAMMAGLOBULINEMIA, X-LINKED]
None	rs3743930 (C;C) ambig

			[omim:FAMILIAL MEDITERRANEAN FEVER]
None	rs28936692 (C;C) ambig

			[omim:HYPOTRICHOSIS-LYMPHEDEMA-TELANGIECTASIA SYNDROME]
None	rs28940273 (G;G) ambig

			[omim:BEST MACULAR DYSTROPHY]
None	rs2268277 (C;G) ambig

			rs7528684 rs3792876 and rs2268277 failed to showed a statistically significant association with rheumatoid arthritis rs2268277, a SNP in the RUNX1 gene, has been associated in a Japanese population with rheumatoid arthritis at at odds ratio of 1.28 (CI = 1.101.48). The study involved 719 cases and 441 controls.
None	rs28931590 (T;T) ambig

			[omim:LEUKEMIA, ACUTE MYELOID]
None	rs28933395 (C;C) ambig

			[omim:RETINITIS PIGMENTOSA 4]
None	rs28935203 (T;T) ambig

			[omim:HEMOPHILIA A]
None	rs28936383 (G;G) ambig

			[omim:MUSCULAR DYSTROPHY, LIMB-GIRDLE, TYPE 2E]
None	rs28933680 (G;G) ambig

			[omim:HEMOPHILIA A]
None	rs891407 (G;G) ambig
			[haplogroup:R]
			[haplogroup:?]
None	rs28936409 (C;C) ambig

			[omim:RIEGER SYNDROME, TYPE 1]
None	rs17250163 (C;C) ambig

			[haplogroup:?]
None	rs17315723 (C;C) ambig
			[haplogroup:I2b]
			[haplogroup:?]
None	rs28933695 (G;G) ambig

			[omim:CONE-ROD DYSTROPHY 6]
None	rs28931583 (G;G) ambig

			[omim:SPHEROCYTOSIS, HEREDITARY, DUE TO BAND 3 TUSCALOOSA]
None	rs28937870 (G;G) ambig

			[omim:COLON CANCER, HEREDITARY NONPOLYPOSIS, TYPE 7]
None	rs4696480 (A;T) ambig

			preterm birth rs4696480 (T-16934A and Arg753Gln) and rs5743708) (Thr399Ile) earlier birth for infants carrying two (-16934TA/AA and 753ArgGln/GlnGln)
None	rs28942113 (C;C) ambig

			[omim:FACTOR V AND FACTOR VIII, COMBINED DEFICIENCY OF]
None	rs9785702 (G;G) ambig

			[haplogroup:?]
None	rs28935177 (A;A) ambig

			[omim:CLEFT PALATE WITH ANKYLOGLOSSIA]
None	rs28941469 (T;T) ambig

			[omim:BEST MACULAR DYSTROPHY]
None	rs28931606 (T;T) ambig

			[omim:POR DEFICIENCY]
None	rs28756986 (C;C) ambig

			[omim:COLON CANCER, HEREDITARY NONPOLYPOSIS, TYPE 7]
None	rs6591255 (T;T) ambig

			asthma
None	rs1801028 (G;G) ambig	normal risk

			rs1801028 is a SNP in the dopamine D2 receptor DRD2 gene. A meta-analysis comprising 27 samples and over 3,707 schizophrenia patients concluded that Cys/Ser heterozygotes, i.e. rs1801028(C;G) genotypes, were at elevated risk for schizophrenia when compared to either homozygote genotype (rs1801028(C;C) or rs1801028(G;G)). The odds ratio was 1.4 (p<0.005). An earlier meta-analysis comprising over 9,000 schizophrenia patients concluded pretty much the same thing: the Cys311 (rs1801028(G)) allele frequency led to an odds ratio of 1.43 (CI: 1.16-1.78, p<0.001) for this risk allele. A study of ~120 Chinese patients with schizophrenia concluded that Cys/Ser heterozygotes may not respond to [risperidone treatment as well as Ser/Ser homozygotes. A paper has been published describing mistakes made i...
None	rs28940584 (C;C) ambig

			[omim:SIALIDOSIS, TYPE II]
None	rs28933381 (G;G) ambig

			[omim:MYOKYMIA]
None	rs28935484 (T;T) ambig

			[omim:ANEMIA, HEREDITARY SIDEROBLASTIC, PYRIDOXINE REFRACTORY]
None	rs4647924 (C;C) ambig

			[omim:MUENKE SYNDROME]
None	rs28929498 (A;A) ambig

			[omim:SQUAMOUS CELL CARCINOMA, BURN SCAR-RELATED, SOMATIC]
None	rs28929479 (T;T) ambig

			[omim:ACROMESOMELIC DYSPLASIA, MAROTEAUX TYPE]
None	rs28935481 (T;T) ambig

			[omim:ADRENAL HYPOPLASIA, CONGENITAL]
None	rs9786915 (C;C) ambig
			[haplogroup:R]
			[haplogroup:?]
None	rs28936689 (C;C) ambig

			[omim:LISSENCEPHALY SEQUENCE, ISOLATED]
None	rs28928874 (A;A) ambig

			[omim:FANCONI-BICKEL SYNDROME]
None	rs11178997 (T;T) ambig

			rs4570625 and rs11178997 in TPH2's regulatory region display preferential transmission [http://archpsyc.ama-assn.org/cgi/content/full/63/10/1103?ck=nck paper] Association with and bipolar disorder in a Northern Swedish, Isolated Population. 182 patients and 364 unrelated control individuals. P = .001 rs11178997 significantly reduced TPH2 transcriptional activity by 22% and 7% in cell lines might have implications for the development and function of the serotonergic system in the brain. [http://www.thieme-connect.com/ejournals/abstract/pharmaco/doi/10.1055/s-2007-991720 paper] Carriers of the A-Allele of rs11178997 showed a decreased cortisol and ACTH stimulation. might be crucial factors for major depression [http://hmg.oxfordjournals.org/cgi/reprint/ddm286v1.pdf pdf paper] associated wit...
None	rs1800471 (C;C) ambig

			rs1800471 encodes a change at codon 25 of the TGFB1 gene. It is reported to predispose several organs to fibrosis, and in relation to Crohn's disease, it was associated with stricturing Crohn's disease (odds ratio 2.63, CI: 1.16-5.88, p=0.01) and a shorter time to intestinal resection (p = 0.06) in a study of several hundred Australian patients.
None	rs28936698 (T;T) ambig

			[omim:PEROXISOME BIOGENESIS DISORDER, COMPLEMENTATION GROUP 3]
None	rs11934801 (G;G) ambig

			[omim:HURLER SYNDROME]
None	rs16980574 (G;G) ambig

			[haplogroup:?]
None	rs28935169 (T;T) ambig

			[omim:HETEROTOPIA, PERIVENTRICULAR]
None	rs28940890 (A;A) ambig

			[omim:ECTOPIA PUPILLAE]
None	rs16980406 (T;T) ambig

			[haplogroup:?]
None	rs28931592 (T;T) ambig

			[omim:DEAFNESS, NEUROSENSORY, AUTOSOMAL RECESSIVE 1]
None	rs28937591 (G;G) ambig

			[omim:DEAFNESS, AUTOSOMAL RECESSIVE 9]
None	rs28928907 (G;G) ambig

			[omim:AMEGAKARYOCYTIC THROMBOCYTOPENIA, CONGENITAL]
None	rs9341312 (T;T) ambig

			[haplogroup:?]
None	rs28934597 (G;G) ambig

			[omim:HEMOCHROMATOSIS]
None	rs28928903 (G;G) ambig

			[omim:WERNER SYNDROME, ATYPICAL]
None	rs2032660 (A;A) ambig

			[haplogroup:?]
None	rs28933394 (C;C) ambig

			[omim:RETINITIS PIGMENTOSA 4]
None	rs28936693 (A;A) ambig

			[omim:HYPOTRICHOSIS-LYMPHEDEMA-TELANGIECTASIA SYNDROME]
None	rs28931572 (A;A) ambig

			[omim:PI NULL(LUDWIGSHAFEN)]
None	rs28936370 (C;C) ambig

			[omim:HYPERINSULINEMIC HYPOGLYCEMIA, FAMILIAL, 1]
None	rs2787094 (G;G) ambig

			rs2787094, a SNP in the ADAM33 gene, has been linked to a predisposition to asthma and bronchial hyperresponsiveness. [PMID 12110844, PMID 14564349]
None	rs28940301 (C;C) ambig

			[omim:ERYTHROCYTOSIS, FAMILIAL, 2]
None	rs28934606 (C;C) ambig

			[omim:VITAMIN D-DEPENDENT RICKETS, TYPE I]
None	rs28940871 (G;G) ambig

			[omim:TAY-SACHS DISEASE]
None	rs28928872 (C;C) ambig

			[omim:VITAMIN K-DEPENDENT COAGULATION DEFECT]
None	rs28937584 (G;G) ambig

			[omim:THYROID CARCINOMA WITH THYROTOXICOSIS]
None	rs28928895 (A;A) ambig

			[omim:PACHYONYCHIA CONGENITA, TYPE 1]
None	rs28932472 (G;G) ambig

			[omim:OBESITY, EARLY-ONSET, SUSCEPTIBILITY TO]
None	rs28933383 (C;C) ambig

			[omim:EPISODIC ATAXIA, TYPE 1]
None	rs28933689 (A;A) ambig

			[omim:THYROXINE-BINDING GLOBULIN DEFICIENCY, PARTIAL, GARY TYPE]
None	rs28930069 (G;G) ambig

			[omim:HYPOKALEMIC PERIODIC PARALYSIS]
None	rs28933688 (C;C) ambig

			[omim:THYROXINE-BINDING GLOBULIN DEFICIENCY, PARTIAL, MONTREAL TYPE]
None	rs9786636 (C;C) ambig
			[haplogroup:F-R]
			[haplogroup:?]
None	rs440446 (G;G) ambig	normal

			rs440446 is a SNP in an intron of the apolipoprotein E APOE gene; it is also known as the IVS1+69 variant. In a study of ~1,000 Chinese patients with various biliary tract conditions, including cancer and gallstones, men carrying a rs440446(C) allele (in dbSNP orientation) had a 1.7x risk of gallstone disease [CI: 1.2-2.4], a 1.8x risk of gallbladder cancer (CI: 1.0-3.3), a 3.7x risk of bile duct cancer (CI: 2.0-7.0), and a 4x risk of ampullary cancer (CI: 1.4-12.4). Note: orientation relative to dbSNP entry is reversed as published.
None	rs13447361 (G;G) ambig

			[haplogroup:?]
None	rs28934577 (A;A) ambig

			[omim:MULTIPLE MALIGNANCY SYNDROME]
None	rs28940569 (G;G) ambig

			[omim:CEROID LIPOFUSCINOSIS, NEURONAL, 8]
None	rs28934003 (T;T) ambig

			Possible [http://www.gtg.com.au/HumanDNATesting/index.asp?menuid=070.020.050.010 commercial test] [omim:GENERALIZED EPILEPSY WITH FEBRILE SEIZURES PLUS, TYPE 2]
None	rs28936408 (A;A) ambig

			[omim:RIEGER SYNDROME, TYPE 1]
None	rs28928892 (C;C) ambig

			[omim:BRACHYDACTYLY, TYPE E]
None	rs28933971 (G;G) ambig

			[omim:TOOTH AGENESIS, SELECTIVE, 3]
None	rs28935482 (C;C) ambig

			[omim:ADRENAL HYPOPLASIA, CONGENITAL]
None	rs28934875 (C;C) ambig

			[omim:LI-FRAUMENI SYNDROME 1]
None	rs7802307 (A;A) ambig

			rs7802307 coronary artery disease 190 affected Asian Indian sibling pairs
None	rs28928900 (C;C) ambig

			[omim:CARDIOMYOPATHY, DILATED, 1A]
None	rs28929473 (T;T) ambig

			[omim:PI NULL(MATTAWA)]
None	rs28940575 (A;A) ambig

			[omim:EPILEPSY, PROGRESSIVE MYOCLONIC 2B]
None	rs28935186 (T;T) ambig

			[omim:PYRUVATE DEHYDROGENASE E1-ALPHA DEFICIENCY]
None	rs28937587 (G;G) ambig

			[omim:ATELOSTEOGENESIS, TYPE III]
None	rs28933372 (C;C) ambig

			[omim:ACROCALLOSAL SYNDROME]
None	rs28939693 (T;T) ambig

			[omim:HOLOPROSENCEPHALY 4]
None	rs3912 (A;A) ambig

			[haplogroup:?]

ALS
13.6	rs3825776 (G;G)	>1.3x risk for ALS

			rs3825776, a SNP in the region of the LIPC gene on chromosome 15, has been associated with the sporadic form of ALS (Lou Gehrig's disease) in a study of 1000+ European patients. The odds ratio for the risk allele rs3825776(G) is 1.34 (CI: 1.12 - 1.46).
28.3	rs13036957 (A;G)

			This SNP was associated with amyotrophic lateral sclerosis (ALS) based on a study of 1,152 patients.
35.0	rs6587852 (A;C)

			rs6587852 is one of 6 SNPs found upstream of an (uncharacterized) gene known as FLJ10986 that have been found to be overrepresented in 1,152 patients with sporadic amyotrophic lateral sclerosis (ALS).
36.7	rs6700125 (C;T)	1.2x increased risk for ALS

			rs6700125 is one of 6 SNPs found upstream of an (uncharacterized) gene known as FLJ10986 that have been found to be overrepresented in patients with sporadic amyotrophic lateral sclerosis (ALS). A genome-wide association study of 1,152 ALS patients determined an allelic odds ratio of 1.38 for the rs6700125(T) allele (CI: 1.16-1.65, p=0.00032). The genotypic odds ratio presented were 1.76 (CI: 1.22-2.55) and 1.2 (CI: 0.83-1.73) for homozygotes and heterozygotes, respectively. * Note: this SNP is in strong linkage disequilibrium with rs6690993 (r²>0.8)
38.3	rs988213 (A;G)

			This SNP was associated with amyotrophic lateral sclerosis (ALS) based on a study of 1,152 patients.
45.0	rs10239794 (C;T)	1.3x risk for ALS

			rs10239794, a SNP in the region of the DPP6 gene on chromosome 7, has been associated with the sporadic form of ALS (Lou Gehrig's disease) in a study of 1000+ European patients. The odds ratio for the risk allele rs10239794(C) is 1.30 (CI: 1.18 - 1.43). A 'CC' haplotype for this SNP and that of it's neighbor rs10260404 is also highly (statistically; p=10e-9) associated with ALS.
48.3	rs10260404 (C;T)	1.2x risk for ALS

			rs10260404, a SNP in the region of the DPP6 gene on chromosome 7, has been associated with the sporadic form of ALS (Lou Gehrig's disease) in a study of 1000+ European patients. The overall odds ratio for the risk allele rs10260404(C) is 1.30 (CI: 1.18-1.43, p=0.017). When broken down by genotype, the odds ratios for heterozygotes are 1.20 (CI: 1.06-1.41), and for rs10260404(C;C) homozygotes, 1.60 (CI: 1.32-1.92). A 'CC' haplotype for this SNP and that of it's neighbor rs10239794 is also highly (statistically; p=10e-9) associated with ALS.
55.0	rs757863 (A;G)

			This SNP was associated with amyotrophic lateral sclerosis (ALS) based on a study of 1,152 patients.
55.9	rs3771150 (C;C)

			This SNP was associated with amyotrophic lateral sclerosis (ALS) based on a study of 1,152 patients.
70.0	rs2836061 (C;C)

			This SNP was associated with amyotrophic lateral sclerosis (ALS) based on a study of 1,152 patients.

Age related macular degeneration
66.7	rs800292 (C;C)	normal

			rs800292 is a SNP in the complement factor H CFH gene; it has been linked to blindness in age related macular degeneration. This SNP is also known as 184G>A or Val62Ile. A haplotype of rs1061170 rs3753394 rs800292 rs1329428 (TGTC) was found to confer a significantly increased likelihood of exudative AMD CFH variations appear to contribute to ARMD in Caucasians, but not in Japanese A study of Chinese AMD patients reports that carriers of both rs11200638 and rs800292 risk alleles pushes the odds ratio for AMD up to 23x. Overall, an 'extremely high' population attributable risk (PAR) of 78% reported for these SNPs.

Alcoholism
30.0	rs27072 (C;T)	normal

			rs27072, a SNP in the dopamine transporter SLC6A3 gene, has been associated with more severe symptoms upon alcohol withdrawal, such as seizures, in a study of 250 Caucasian alcohol-dependent patients. Two haplotypes appear to be tagged by this SNP and a neighbor, rs27048.
30.0	rs27048 (C;C)	2x risk of severe alcohol withdrawal

			rs27048, a SNP in the dopamine transporter SLC6A3 gene, has been associated with more severe symptoms upon alcohol withdrawal, such as seizures, in a study of 250 Caucasian alcohol-dependent patients. Two haplotypes appear to be tagged by this SNP and a neighbor, rs27072.
68.3	rs1799971 (A;A)

			The rs1799971(G) allele in exon 1 of the mu opiod receptor gene causes the normal amino acid at residue 40, asparagine, to be replaced by aspartic acid. Carriers of at least one rs1799971(G) allele appear to have stronger cravings for alcohol than carriers of two rs1799971(A) alleles, and are thus hypothesized to be more at higher risk for alcoholism. However, the research results are quite mixed, and there are other studies both agreeing or disagreeing with this finding [PMID 15525999, PMID 9399694, PMID 12960749]
77.6	rs1076560 (C;C)

			rs1076560 is located in intron 6 of the dopamine receptor D2 gene. In one study of Japanese males, rs1076560(A) alleles were 1.3 fold more associated with Alcoholism than the rs1076560(C) alleles. The DRD2 risk allele A was more prevalent in the alcoholic patients than in the healthy controls. These data identify rs1076560 as a potentially important variable in the development of alcoholism.

Alzheimer's disease
1.7	rs4877365 (A;A)

			rs4877365 has been linked to Alzheimer's disease
15.0	rs4878104 (T;T)

			linked to Alzheimer's disease
31.7	rs2227564 (C;T)

			rs2227564 A functional polymorphism within plasminogen activator urokinase (PLAU) is associated with Alzheimer's disease . *rs2227564 distribution of four tagSNPs (rs2227562 in intron 5, rs2227564 in exon 6, rs2227571 in intron 9, and rs4065 in 3'UTR) in the PLAU gene in a large case-control study of Alzheimer's disease [omim:ALZHEIMER DISEASE, LATE-ONSET, SUSCEPTIBILITY TO]
48.3	rs669 (A;G)	possibly increased risk for Alzheimers

			rs669 is a SNP in the alpha-2-macroglobulin A2M gene. In dbSNP orientation, the rs669(A) allele encodes an isoleucine, and the rs669(G) allele encodes a valine; the SNP is also known as the Ile/Val variant. On its own, rs669 was not seen to reprocudibly and independently increase risk for Alzheimer's disease in several studies of ~200 Italian patients. However, the T-C-A haplotype of rs12316150-rs1050283-rs669 was associated with both early- and late-onset Alzheimer's disease. The majority of the disease risk from this haplotype was based on rs1050283. The original 2004 study of 148 Italian sporadic AD patients yielded an odds ratio for the rs669(G;G) genotype (as oriented in dbSNP orientation) of 3.81 (CI: 1.66-8.75). The presence of rs2333227(C;C), in addition to rs669(G;G), appears to s...
65.0	rs11030104 (A;A)

			Alzheimer's disease risk for non ApoE4 carriers is affected by the heterozygous form of rs6265, as well as the diplotypes of rs6265, rs11030104, and rs2049045.
68.3	rs6265 (G;G)	?

			This snp in BDNF seems to affect the risk of Alzheimer's disease. Alzheimer's disease risk for non ApoE4 carriers is affected by the heterozygous form of rs6265, as well as the diplotypes of rs6265, rs11030104, and rs2049045. The A allele may also be protective against depression when subjected to repeated defeat [http://originsgenomeresources.net/musings/?p=66 blog summary]
68.3	rs2049045 (G;G) ambig

			Alzheimer's disease risk for non ApoE4 carriers is affected by the heterozygous form of rs6265, as well as the diplotypes of rs6265, rs11030104, and rs2049045.
None	rs908832 (G;G)	normal
			This is the genotype of User:Watson
			This SNP, a synonymous substitution in the ABCA2 gene, has been linked to early onset Alzheimer's disease with an odds ratio of 3.8 for disease development in carriers of the A allele (in dbSNP orientation) compared to controls (95% CI 2-7.3), based on a study of ~400 Caucasian patients. Subsequently, this association was replicated in a Western European population (n=291, p=0.008), but not in a second sample from Southern Europe. rs908832 was not polymorphic in a Japanese sample. Furthermore, rs908832 was not associated with either serum cholesterol levels or with the risk for coronary artery disease, but did seem to be related to cholesterol levels in the cerebrospinal fluid.
None	rs2254958 (-;-)

			While the ApoE4 allele (rs429358(C)) is widely accepted as the predominant genetic risk factor for Alzheimer's disease, there are likely to be numerous other factors, both genetic and environmental, associated to lesser degrees with susceptibility to the disease. Genes influencing the immune system, and in particular susceptibility to viral infections such as herpes, may be among such factors. This SNP, located in the promoter region of the EIF2AK2 gene and thus implicated in the activation of HIV and HSV-1 viruses, is seen more commonly in ~300 Alzheimer patients than in the same number of controls. The risk allele is rs2254958(C). The odds ratio is reported to be 1.61 (CI: 1.02-2.55) for rs2254958(C;C) homozygotes, and 1.24 (CI: 0.80-1.93) for rs2254958(C;T) heterozygotes, compared with...

Ankylosing spondylitis
20.0	rs1343151 (T;T)	0.8x lower risk for spondylitis

			rs1343151 is one of several SNPs in the IL23R gene that has been shown in a large (over 1,000 Caucasian patients) study to be associated with ankylosing spondylitis. The odds ratio is 0.8 (p=1.0x10e-5).[PMID 17952073, PMID 18037607]
30.0	rs10489629 (G;G)	0.83x lower risk for spondylitis

			rs10489629 is one of several SNPs in the IL23R gene that has been shown in a large (over 1,000 Caucasian patients) study to be associated with ankylosing spondylitis. The odds ratio is 0.83 (p=0.00014).[PMID 17952073, PMID 18037607]
40.0	rs30187 (C;T)	1.4x higher risk for spondylitis

			rs30187 is one of several SNPs in the ARTS1 gene that has been shown in a large (over 1,000 Caucasian patients) study to be associated with ankylosing spondylitis. The odds ratio is 1.40 (p=3.4x10e-10).[PMID 17952073, PMID 18037607]
51.7	rs1004819 (C;C)	common

			SNP rs1004819, in the IL23R gene, is associated with increased risk for Crohn's disease in both Jewish and non-Jewish populations. The same risk allele is also reported to increase the risk for developing ankylosing spondylitis, based on a large study of over 1,000 Caucasian patients. The odds ratio is 1.2 (p=8.8x10e-5).[PMID 17952073, PMID 18037607] significant associations with rs1004819, rs7517847, and rs11209026. Having any CARD15 variant was associated with a significant risk for CD (P < 0.0001).
53.3	rs10889677 (C;C)	1x risk for certain autoimmune diseases; 2.3x risk for Graves disease

			SNP rs10889677, in the IL23R gene, is associated with increased risk for Crohn's disease in both Jewish and non-Jewish populations. The same risk allele for this SNP has been associated with increased risk for ankylosing spondylitis in a large study of over 1,000 Caucasian patients. The odds ratio is 1.3 (p=1.3x10e-6).[PMID 17952073, PMID 18037607] In a study of 216 North American patients with Graves' disease, the C allele of rs10889677 was 2.03x overrepresented (p=1.3x10⁴), and the homozygous rs10889677(C;C) genotype was also overrepresented (2.36x; p=1.4x10^-4) in Graves ophthalmopathy patients.
58.3	rs10050860 (C;C)	normal risk

			rs10050860 is one of several SNPs in the ARTS1 gene that has been shown in a large (over 1,000 Caucasian patients) study to be associated with ankylosing spondylitis. The odds ratio is 0.71 (p=7.7x10e-9).[PMID 17952073, PMID 18037607]
86.7	rs11465804 (T;T)	normal risk

			rs11465804 is one of several SNPs in the IL23R gene that has been shown in a large (over 1,000 Caucasian patients) study to be associated with ankylosing spondylitis. The odds ratio is 0.68 (p=0.0002).[PMID 17952073, PMID 18037607]
88.1	rs11209026 (G;G)	common

			A relatively rare allele at SNP rs11209026, in the IL23R gene, appears to provide a fairly strong protective effect against the development of Crohn's disease in both Jewish and non-Jewish populations. Note that in this study the (A;A) and (A;G) genotypes were combined for statistical reasons (there were too few (A;A) individuals to study by themselves), so the risk is shown as equal for both. associated With Inflammatory Bowel Diseases but Not With Celiac Disease rs11209026 had a protective effect for IBD in the case-control analysis (odds ratio [OR] 0.19, 95% confidence interval [CI] 0.10-0.37, P= 6.6E-09). Both CD (OR 0.14, CI 0.06-0.37, P= 3.9E-07) and UC (OR 0.33, CI 0.15-0.73, P= 1.4E-03) were associated with IL23R. rs2241880 was associated with CD susceptibility (OR 1.36, CI 1.12-...

Asthma
35.0	rs1695 (A;A)	normal

			This snp, in the GSTP1 gene influences asthma risk mentioned in this [http://news.bbc.co.uk/2/hi/uk_news/scotland/tayside_and_central/5251968.stm bbc article] also known as GSTP1Val105, or GSTP1 Ile105Val This [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16882827&query_hl=1&itool=pubmed_docsum research paper] shows that 13- to 21-year-olds exposed to tobacco smoke at home, with this mutation had more severe asthma than those without the mutation. Several papers published findings associating GSTP1 Ile105Val genotypes with bronchial, childhood, or atopic asthma. Note that some studies, however, have not observed any association between this SNP and asthma in certain populations , or even more paradoxically, have observed that rs1695(G;G)...
43.3	rs324981 (A;T) ambig

			asthma related influences sleep patterns [http://originsgenomeresources.net/musings/?p=62] [omim:ASTHMA SUSCEPTIBILITY 2]
52.5	rs2278206 (T;T)	1.16x increased risk for asthma

			A study of ~170 families led to a slight association between rs2278206 and atopic asthma. The risk genotype - in dbSNP orientation, not as published - is rs2278206(T;T). Conversely, the rs2278206(C;C) genotype was rarely (odds ratio 0.13) seen in patients with atopic asthma.
53.3	rs977785 (C;C)	increased risk

			rs977785, a SNP purported to be in the promoter of the LY86 gene, is reported to be associated with mite-sensitive allergies in children, based on a study of 500+ Taiwanese patients. The allele that is underrepresented (and thus protective?) is the minor allele, which in dbSNP orientation is rs1334710(A).
60.0	rs7216389 (C;T)	not clear

			rs7216389, a SNP in the ORMDL3 gene on chromosome 17q21, was associated with susceptibility to childhood asthma in a study of ~1,000 British patients. The variation appears to be linked to altered levels of the ORMDL3 mRNA, which was shown in a cohort study of ~5,000 British and German patients to be correlated to childhood asthma.
60.0	rs1051931 (G;G)

			asthma related [omim:ASTHMA AND ATOPY, SUSCEPTIBILITY TO]
85.0	rs1805018 (T;T)

			asthma related [omim:ASTHMA AND ATOPY, SUSCEPTIBILITY TO]

Atrial fibrillation
79.7	rs2200733 (C;C)	1.4x increased risk of atrial fibrillation

			Two SNPs from chromosome 4q25, rs2200733 and rs10033464, were found to be associated with atrial fibrillation in a study of both European and Asian populations. The odds ratio associated with one or more copies of either risk allele was ~1.4x.
80.0	rs10033464 (G;G)	1.4x increased risk of atrial fibrillation

			Two SNPs from chromosome 4q25, rs2200733 and rs10033464, were found to be associated with atrial fibrillation in a study of both European and Asian populations. The odds ratio associated with one or more copies of either risk allele was ~1.4x.

Autism
27.1	rs2710102 (T;T)

		rs2710102, a common SNP in the CNTNAP2 gene, was found to be significantly associated (p<0.028) with a delayed onset of speech, as measured by the age at which a child speaks their first words, in children with autism. This effect is primarily seen in males, perhaps correlated with the 4-5x overrepresentation of males with autism compared with females. The confirmatory Stage 2 study was performed on 304 independent parent-child trios. However, the risk allele and the degree to which speech is delayed per genotype is unclear as published and awaits clarification by the authors.

Behcet's disease
0.0	rs2476601 (A;A)	>2x risk for T1D, RA, Addison's

			This SNP, located in the PTPN22 gene and also known as R620W, or 1858C>T, may influence Rheumatoid Arthritis and other autoimmune diseases, including but not limited to, multiple sclerosis, Crohn's disease, celiac disease and type-1 diabetes. The risk allele (in dbSNP orientation) is rs2476601(A). Note that rs6679667 and rs2476601 are reported to be perfectly correlated, so SNP determination of one predicts the other. In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for type-1 diabetes for this SNP was recalculated to be 1.98 (CI 1.822.15). rs2476601 was confirmed in another 2007 study to be a risk factor for RA . * confirms the association of rs2476601 rheumatoid arthritis * two copies of the PTPN22 R620W allele more than doubles the ris...

Bipolar disorder
13.3	rs131690 (A;A)	normal risk

			rs131690, a SNP in the BCR gene on chromosome 22, has been associated with increased risk for bipolar disorder. The odds ratio for carriers of the minor allele (G) are reported as 1.50 (CI:1.14 - 2.03, p=0.0063) based on a study of 171 Japanese patients.
20.3	rs7757037 (A;A)	0.63x decreased risk for bipolar disorder

			rs7757037, a SNP in the FKBP5 gene, is associated with increased risk for bipolar disorder in a study of 500+ Caucasian patients. The most common allele, rs7757037(G), was associated with highest risk. Giving that allele a relative odds ratio of 1.0, the odds for the (A;G) and (A;A) genotypes were 0.68x (CI:0.53-0.87, p=0.007) and 0.63x (CI: 0.45-0.89, p=0.007).
21.7	rs534654 (C;T)

			Along with rs6442925 and rs1534891, this SNP, rs534654, is part of a 3-SNP (multi-locus) interaction that is associated with bipolar disorder.
22.0	rs140504 (A;G)	1.4x increased risk for bipolar disorder

			rs140504, a SNP in the BCR gene on chromosome 22, has been associated with increased risk for bipolar disorder. The odds ratio for carriers of the minor allele (G) are reported as 1.45 (CI:1.11 - 1.84, p=0.0054) based on a study of 171 Japanese patients.
35.6	rs6458307 (C;T)	0.8x risk

			rs6458307 has been reported in a large study to be associated with bipolar disorder. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated with heterozygotes is 0.84 (CI 0.75-0.96), and for homozygotes, 1.39 (CI 1.13-1.69).
43.3	rs3847953 (G;G)

			rs3847953 and rs933399 associated with bipolar disorder
44.1	rs4276227 (C;C)	1.5x risk

			rs4276227 has been reported in a large study to be associated with bipolar disorder. The risk allele (oriented to the dbSNP entry) is (C); the odds ratio associated with heterozygotes is 1.2 (CI 0.99-1.46), and for homozygotes, 1.49 (CI 1.23-1.81).
59.3	rs7570682 (G;G)	normal

			rs7570682 has been reported in a large study to be associated with bipolar disorder. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.23 (CI 1.09-1.40), and for homozygotes, 1.64 (CI 1.28-2.12).
79.7	rs6442925 (C;C)

			Along with rs534654 and rs1534891, this SNP, rs6442925, is part of a 3-SNP (multi-locus) interaction that is associated with bipolar disorder.
80.0	rs683395 (T;T)	normal

			rs683395 has been reported in a large study to be associated with bipolar disorder. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.47 (CI 1.26-1.71), and for homozygotes, 1.3 (CI 0.69-2.46).
81.4	rs1534891 (C;C)

			Along with rs6442925 and rs534654, this SNP, rs1534891, is part of a 3-SNP (multi-locus) interaction that is associated with bipolar disorder.
None	rs420259 (C;T)	2x risk

			Linked to bipolar disorder in one of the most comprehensive studies to date (2007). Risk allele with reference to dbSNP orientation is reported to be (T), with either one or two copies leading to an odds ratio of 2 (CI 1.6-2.7).
None	rs11178997 (T;T) ambig

			rs4570625 and rs11178997 in TPH2's regulatory region display preferential transmission [http://archpsyc.ama-assn.org/cgi/content/full/63/10/1103?ck=nck paper] Association with and bipolar disorder in a Northern Swedish, Isolated Population. 182 patients and 364 unrelated control individuals. P = .001 rs11178997 significantly reduced TPH2 transcriptional activity by 22% and 7% in cell lines might have implications for the development and function of the serotonergic system in the brain. [http://www.thieme-connect.com/ejournals/abstract/pharmaco/doi/10.1055/s-2007-991720 paper] Carriers of the A-Allele of rs11178997 showed a decreased cortisol and ACTH stimulation. might be crucial factors for major depression [http://hmg.oxfordjournals.org/cgi/reprint/ddm286v1.pdf pdf paper] associated wit...

Breast cancer
30.0	rs12255372 (G;T)	?
			This is the genotype of User:Watson
			This SNP is in the TCF7L2 gene, and has been linked to type-2 diabetes, breast cancer and aggressive prostate cancer. is the paper which links it to Breast cancer. It suggests the T allele as increasing risk. reports the association of rs12255372 and rs7903146 with Type-2 diabetes in a Finnish sample. rs12255372 Common variants (rs12255372 and rs7903146) in TCF7L2 seem to be associated with an increased risk of diabetes among persons with impaired glucose tolerance Considered for type-2 diabetes with rs7903146 rs12255372 rs10885406. Associated in a study of ~1000 Hispanic-Americans with reduced insulin secretion as measured by acute insulin response and adjusted for the degree of insulin sensitivity (p = 0.036). In a study of 1,457 prostate cancer cases and 1,351 controls, while there w...
35.0	rs3731239 (T;T)	normal risk

			rs3731239 shows a slight protective association against breast cancer in a British study involving ~2300 patients. The odds ratio for the (C;C) vs (T;T) homozygotes is 0.90 (CI: 0.79-1.03, p=0.013).
40.0	rs1219648 (A;G)	1.20x risk for breast cancer
			This is the genotype of User:Watson
			Based on a study of ~2500 female patients of European ancestry with sporadic postmenopausal breast cancer, this SNP in the FGFR2 showed the greatest risk. The risk allele is rs1219648(G), with a pooled odds ratio of 1.64 (CI:1.42-1.90) for rs1219648(G;G) homozygotes, and an odds ratio of 1.20 (CI: 1.07-1.42) for rs1219648(A;G) heterozygotes, compared with rs1219648(A;A) homozygotes. rs1219648 represents the SNP in the FGFR2 gene with the strongest association with breast cancer. However, nearby SNPs are almost as predictive. In particular, the following SNP alleles all have linkage values of 0.96 or greater with the rs1219648(G) allele in European populations: rs2981579(A) rs2420946(T) *rs11200014(A) An experimental rationale is presented indicating that this SNP is part of a haplotype t...
43.3	rs16942 (A;A)

			This SNP, a variant in the BRCA1 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (G).
43.3	rs1799966 (A;A)

			This SNP, a variant in the BRCA1 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (G).
48.3	rs997669 (A;G)	?

			rs997669 shows an association with breast cancer in a British study involving ~2300 patients. The odds ratio for the (G;G) vs (A;A) homozygotes is 1.18 (CI: 1.04-1.34, p=0.003).
48.3	rs203462 (A;G)

			Linked to breast cancer [omim:LONGEVITY, REDUCED]
49.1	rs351855 (C;T)	?

			The Arg form of this snp is likely to cause a hard to treat version of breast cancer. It determines the efficacy of Herceptin. This is the snp described in as the FGFR4-Gly388Arg mutation. [omim:CANCER PROGRESSION AND TUMOR CELL MOTILITY]
51.7	rs3803662 (C;C)	normal

			rs3803662, a SNP associated with the TNRC9 gene, was one of the four strongest associating SNPs found in a genome-wide association study of over 4,000 breast cancer samples. rs3803662(T;T) have a 1.64-fold greater risk of estrogen receptor-positive tumors In a study of 1,267 breast cancer patients, rs3803662 heterozygote carriers and minor allele homozygote carriers were more likely to be diagnosed before the age of 60 years (p = 0.025) relative to major allele homozygote carriers. breast cancer *rs2981582, rs3803662, and rs889312) showed weak but significant associations with ER-negative disease, the strongest association being for rs3803662 in TNRC9 (1.14 (1.09-1.21))
51.7	rs144848 (G;T)

			This SNP, a variant in the BRCA2 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (G). [omim:BREAST CANCER, TYPE 2, SUSCEPTIBILITY TO]
51.7	rs3817198 (C;T)

			rs3817198, a SNP associated with the LSP1 gene, was one of the four strongest associating SNPs found in a genome-wide association study of over 4,000 breast cancer samples.
61.7	rs1042522 (G;G) ambig	(?)longer lifespan?

			This SNP, a variant in the TP53 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (C). The minor allele encodes an arginine at position 72 of the protein (where there's normally a proline), and the SNP is commonly called the Arg72 variant, although P72R is also common in the literature. Minor allele homozygotes, i.e. rs1042522(C;C) genotypes, live on average 3 years longer than major allele (G;G) homozygotes, based on a study of 9,200+ Danish individuals. The increased longevity is speculate...
63.3	rs34330 (C;C)	normal risk

			Category:interesting rs34330 shows an association with breast cancer in a British study involving ~2300 patients. The odds ratio for the (T;T) vs (C;C) homozygotes is 1.22 (CI: 1.02-1.47, p=0.013). found a significant association between rs34330 (-79C/T) and prostate cancer see also [http://www.genome.jp/dbget-bin/www_bget?omim+176807 omim 176807]
68.3	rs2273535 (A;A) ambig	common

			SNP rs2273535, also known as F31I or Phe31Ile, has been associated with increased risk for several cancers, in most cases when individuals are homozgyous for the risk allele, rs2273535(T), as oriented to the dbSNP entry. A meta-analysis of almost 10,000 cases of breast, colon, ovarian, prostate, lung, esophageal and non-melanoma skin cancer, compared to an equal number of Caucasian controls, determined the following risks (i.e., odds ratios, OR) : For colorectal cancer: OR for homozygotes of 1.5 (CI: 1.14-1.99) For breast cancer: OR for homozygotes of 1.35 (CI: 1.12-1.64) *For any of the cancer types studied: OR for heterozygotes of 1.10 (CI: 1.03-1.18), OR for homozygotes of 1.40 (CI: 1.22-1.59) In a Chinese population, breast cancer risk for rs2273535(T;T) homozygotes compared to the o...
76.7	rs1045485 (G;G) ambig

			also known as D302H [PMID 15601643, PMID 17018785, PMID 17293864] Several large studies indicate that the (C) allele of this SNP, located in exon 10 of the CASP8 gene, may reduce the risk of Breast Cancer in a dose dependent manner [http://www.infozine.com/news/stories/op/storiesView/sid/20982/ article] [http://cancergenetics.wordpress.com/2007/10/05/caspase-8-story-breast-cancer/ cancergenetics] showed '''no association''' with ovarian cancer risk 4,624 invasive epithelial ovarian cancer cases and 8,113 controls of white non-Hispanic origin ovarian cancer
83.3	rs3218536 (G;G)	normal risk

			rs3218536, a relatively rare SNP also known as Arg188His located in the DNA-repair gene XRCC2, is associated with a lowered risk for breast cancer based on a study of 1,100 Cypriot women. The odds ratio for the His-encoding rs3218536(A) allele carriers is homozygote is 0.79, CI: 0.62-1.00, p=0.05. rs3218536(A) carriers also appear to be at lower risk for epithelial ovarian cancer. In a study of ~1,600 cases, the odds ratio for rs3218536(A;G) heterozygotes was 0.8 (CI: 0.7-1.0) and for the (quite rare) rs3218536(A;A) homozygotes 0.3 (0.1-0.9).
90.0	rs1800058 (C;C)

			This SNP, a variant in the ATM gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (T).
91.7	rs1799950 (A;A)	normal breast cancer risk

			This SNP, a variant in the BRCA1 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. This particular SNP, rs1799950, was actually the only SNP of the 25 to have an increased odds ratio for breast cancer to be over 1.5 in carriers and to also be present at a minor allele frequency of over 5%. The odds ratio calculated was 1.72 (P = 0.0002). The risk (minor) allele is (G).
95.0	rs1801270 (C;C)	increased risk for lung cancer

			rs1801270 is a SNP known as p21 codon 31, although the gene now known to code for the p21 protein is termed CDKN1A, and has also been known as WAF1 and CIP1. Along with p53 codon 72 (rs1042522), it is one of the best studied SNPs due to its role in increased tumor susceptibility (and thus cancer). A study of ~150 lung cancer patients in Sweden found that the rs1801279(A) allele, encoding the amino acid Arg at codon 31, represented the risk allele (odds ratio 1.7, CI: 1.0-2.9), compared to healthy individuals. The difference was even more striking when compared to patients with chronic obstructive pulmonary disease (COPD), in which case the odds ratio was over 5. [omim:CIP1/WAF1 TUMOR-ASSOCIATED POLYMORPHISM 1]
95.0	rs1800056 (T;T)

			This SNP, a variant in the ATM gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (C).
96.6	rs2854344 (G;G)	1.25x risk of developing ovarian cancer

			associated with breast cancer risk and ovarian cancer More specifically: carriers of two rs2854344(A) alleles have a 25% reduced risk of developing ovarian cancer compared to carriers of two rs2854344(G) alleles, in a survey of ~5,000 women from the US, UK, and Denmark. showed '''no association''' with ovarian cancer risk 4,624 invasive epithelial ovarian cancer cases and 8,113 controls of white non-Hispanic origin ovarian cancer
96.7	rs4987117 (C;C)

			This SNP, a variant in the BRCA2 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (T).
100.0	rs2227945 (A;A)

			This SNP, a variant in the BRCA1 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (G).
None	rs17879961 (A;A)

			This SNP, a variant in the CHEK2 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (C). rs17879961 one of 3 SNPs associated with increased risk of lung cancer
None	rs361525 (G;G)	complex; generally normal risk

			rs361525 is also known as the TNF -238 SNP, and occasionally the rs361525(A) allele is referred to as 238.2 (with the more common (G) allele being 238.1). This SNP has been linked to a wide variety of conditions: * A large study of over 5,000 Caucasian women found that rs361525(A) allele carriers were at somewhat elevated risk for breast cancer compared to the (G;G) genotype, with an odds ratio per allele of 1.18, CI: 1.04-1.35, p(trend)= 0.008. * A study of ~100 allogeneic haematopoietic stem cell transplant recipients in Brazil concludes that graft versus host disease (GVHD) is about twice as frequent if either the donor or the recipient are rs361525(A) carriers. * Children who are rs361525(G;G) homozygotes may be more prone to ear infections; adjusted odds ratio 2.29, p=0.03). * The rs3...

Cancer
68.3	rs2273535 (A;A) ambig	common

			SNP rs2273535, also known as F31I or Phe31Ile, has been associated with increased risk for several cancers, in most cases when individuals are homozgyous for the risk allele, rs2273535(T), as oriented to the dbSNP entry. A meta-analysis of almost 10,000 cases of breast, colon, ovarian, prostate, lung, esophageal and non-melanoma skin cancer, compared to an equal number of Caucasian controls, determined the following risks (i.e., odds ratios, OR) : For colorectal cancer: OR for homozygotes of 1.5 (CI: 1.14-1.99) For breast cancer: OR for homozygotes of 1.35 (CI: 1.12-1.64) *For any of the cancer types studied: OR for heterozygotes of 1.10 (CI: 1.03-1.18), OR for homozygotes of 1.40 (CI: 1.22-1.59) In a Chinese population, breast cancer risk for rs2273535(T;T) homozygotes compared to the o...

Cannabis dependence
43.3	rs806380 (A;G)

		This snp, located in intron 2 of the central cannabinoid receptor CNR1 gene, has been linked to cannabis dependence. The (G) allele is reported to have a protective effect, and is a defining part of a haplotype that is associated with lower odds of developing cannabis dependence. The (A) allele is more common in all populations studied.

Celiac disease
48.3	rs3184504 (C;T)	increased risk for celiac disease

			rs3184504 is a nonsynonymous SNP in the SH2B3 gene, and it is also known as R262W. In a recent (2008) study of non-HLA SNP associations of 1600+ celiac disease patients, this SNP was considered one of the most significant. The odds ratio for the minor allele was 1.19 (CI:1.101.30, p=1.33x10e-7). rs653178, another SNP in strong linkage disequilibrium (r²>0.99) with rs3184504, was also associated with celiac disease. associated with type-1 diabetes
62.7	rs6822844 (G;G)

			association with rheumatoid arthritis and type-1 diabetes point to a general risk locus for autoimmune diseases. Also, of SNPs outside the HLA region, this SNP and one other (rs13119723) in the region of the IL21 gene showed the strongest association with celiac disease in a study of ~800 Caucasian patients and a meta-analysis of two further populations.
71.7	rs13119723 (A;A)

			Of SNPs outside the HLA region, this SNP and one other (rs6822844) in the region of the IL21 gene showed the strongest association with celiac disease in a study of ~800 Caucasian patients and a meta-analysis of two further populations.

Colon cancer
68.3	rs2273535 (A;A) ambig	common

			SNP rs2273535, also known as F31I or Phe31Ile, has been associated with increased risk for several cancers, in most cases when individuals are homozgyous for the risk allele, rs2273535(T), as oriented to the dbSNP entry. A meta-analysis of almost 10,000 cases of breast, colon, ovarian, prostate, lung, esophageal and non-melanoma skin cancer, compared to an equal number of Caucasian controls, determined the following risks (i.e., odds ratios, OR) : For colorectal cancer: OR for homozygotes of 1.5 (CI: 1.14-1.99) For breast cancer: OR for homozygotes of 1.35 (CI: 1.12-1.64) *For any of the cancer types studied: OR for heterozygotes of 1.10 (CI: 1.03-1.18), OR for homozygotes of 1.40 (CI: 1.22-1.59) In a Chinese population, breast cancer risk for rs2273535(T;T) homozygotes compared to the o...

Colorectal cancer
18.3	rs6983267 (G;G)	1.58x risk for prostate cancer; also colon cancer

			rs6983267 is a SNP on chromosome 8q24, associated with increased risk for prostate cancer in several studies. In studies dividing the 8q24 region, this SNP falls in region 3. In a study of over 3,600 Caucasians with prostate cancer, rs6983267 is one of five SNPs used (with family history as a sixth factor) to cumulatively predict overall risk. On their own, the rs6983267(G;G) and (G;T) risk genotypes yield an odds ratio for developing prostate cancer of 1.37 (CI: 1.18-1.59, p=3.4-10e-5) and may account for 22.2% of population attributable risk. The increased risk of developing prostate cancer associated with rs6983267 now appears to be independent of the risk associated with it's close neighbor, rs1447295. The odds ratio for heterozygotes is estimated to be 1.26 (CI: 1.13 - 1.41), and for ...
23.3	rs7903146 (C;C)	normal form

			This SNP in TCF7L2 influences the risk of Type-2 diabetes (T2D). rs7903146(C;T) rs7903146(T;T) strongly predicted future type-2 diabetes. Considered in context with rs7903146 rs12255372 rs10885406. Note: this is one of two SNPs within the TCF7L2 gene that have been reported to be associated with type-2 diabetes, the other being rs4506565. They have approximately equal power to estimate risk for type-2 diabetes, and the results from one correlate 92% of the time with the other. [http://medicine.plosjournals.org/perlserv/request=get-documentamp?request=get-document&doi=10.1371/journal.pmed.0030374 Full text of the paper] is available from from Plos Medicine. Or from NCBI as . TCF7L2 polymorphisms and progression to diabetes in the Diabetes Prevention Program. reconfirmed in a diverse pop...
26.7	rs4939827 (T;T)	1x normal risk for colorectal cancer

			rs4939827 is one of 3 SNPs in the SMAD7 gene associated with risk for colorectal cancer, based on a large study (7,400+ cases) conducted in the UK. The odds ratios show a decreased risk for the minor rs4939827(C) allele; the OR for (C;C) homozygotes is 0.73 (CI: 0.66-0.8), and for (C;T) heterozygotes 0.86 (CI: 0.79-0.92), overall p=1x10^-12.
35.0	rs12953717 (C;C)	1x normal risk for colorectal cancer

			rs12953717 is one of 3 SNPs in the SMAD7 gene associated with risk for colorectal cancer, based on a large study (7,400+ cases) conducted in the UK. The odds ratios show an increased risk for the minor rs12953717(T) allele; the OR for (T;T) homozygotes is 1.37 (CI: 1.25-1.5), and for (C;T) heterozygotes 1.11 (CI: 1.03-1.2), overall p=9x10^-12.
51.7	rs4464148 (T;T)	1x normal risk for colorectal cancer

			rs4464148 is one of 3 SNPs in the SMAD7 gene associated with risk for colorectal cancer, based on a large study (7,400+ cases) conducted in the UK. The odds ratios show an increased risk for the minor rs4464148(C) allele; the OR for (C;C) homozygotes is 1.35 (CI: 1.2-1.51), and for (C;T) heterozygotes 1.10 (CI: 1.09-1.21), overall p=7x10^-8.
66.7	rs1047972 (C;C)

			influences mitosis associated with cancer * breast cancer * colorectal cancer * gastric cancer
68.3	rs2273535 (A;A) ambig	common

			SNP rs2273535, also known as F31I or Phe31Ile, has been associated with increased risk for several cancers, in most cases when individuals are homozgyous for the risk allele, rs2273535(T), as oriented to the dbSNP entry. A meta-analysis of almost 10,000 cases of breast, colon, ovarian, prostate, lung, esophageal and non-melanoma skin cancer, compared to an equal number of Caucasian controls, determined the following risks (i.e., odds ratios, OR) : For colorectal cancer: OR for homozygotes of 1.5 (CI: 1.14-1.99) For breast cancer: OR for homozygotes of 1.35 (CI: 1.12-1.64) *For any of the cancer types studied: OR for heterozygotes of 1.10 (CI: 1.03-1.18), OR for homozygotes of 1.40 (CI: 1.22-1.59) In a Chinese population, breast cancer risk for rs2273535(T;T) homozygotes compared to the o...
71.7	rs4779584 (C;C)	average

			A study of 7000+ UK patients with colorectal cancer identified two SNPs that increase disease risk, one of which is rs4779584. Inheriting the rs4779584(T) risk allele is estimated to increase overall risk odds by 1.26x (CI: 1.19-1.34, p=4x10e-14). When analyzing data between genotypes, the odds ratios reported for heterozygotes was 1.23x (CI:1.13-1.33), and for rs4779584(T;T) homozygotes, 1.70 (CI: 1.41-2.04). Inheriting the risk variant at both SNP loci (i.e. rs4779584 and rs6983267) is estimated to increase the overall risk of developing colorectal cancer about 3 fold. The authors of this study are quoted as saying that 'the lifetime risk [of bowel cancer] is about 5% in the UK so it's going up to 7% or so if you've got both bad copies of a variant.' [http://www.nature.com/ng/journal/vao...
None	rs2306536 (C;C)	average

			rs2306536, a SNP in the CHFR gene, was found to be significantly associated with a lower risk of colorectal cancer (odd ratio 0.53, CI: 0.30-0.94), and to be significantly correlated with the absence of distant metastases, in a case/control study of ~500 Korean patients.

Crohn's disease
21.7	rs5051 (C;C)	normal risk

			rs5051 is a SNP in the promoter of the angiotensin AGT gene, and presumably due to it's tight linkage with rs699, the rs5051(T) allele - as oriented to the dbSNP entry, not as published - has been associated with increased risk for hypertension and complications thereof. rs699(T) is associated with higher plasma angiotensinogen levels, and therefore the increased risk of essential hypertension. The frequency of the rs699(T) allele is also generally higher in African populations compared to Caucasian populations, correlating to the higher incidence of hypertension in African population. rs5051 is also known as 'A-6G'. For more details, see rs699. rs5051(T;T) homozygotes have been reported to be at increased risk for Crohn's disease, as based on one cohort of ~350 Australian patients. The od...
26.7	rs6601764 (T;T)	normal

			rs6601764 has been reported in a large study to be associated with Crohn's disease. The risk allele (oriented to the dbSNP entry) is (C); the odds ratio associated with heterozygotes is 1.16 (CI 1.01-1.33), and for homozygotes, 1.52 (CI 1.28-1.80).
28.3	rs2241880 (C;C)	2x risk

			rs2241880, a SNP in the ATG16L1 gene encoding a threonine to alanine substitution ('T300A') in a protein known to be involved in the function of the epithelial cells lining the intestine, has been associated with Crohn's disease in several recent studies. [PMID 17200669, PMID 17435756] In another recent (2007) report, rs2241880 is confirmed to be associated with both Crohn's disease and ileal disease, but additionally, the authors calculate risk for individuals who are homozygotes for this SNP plus 2 others (in the IBD5 and NOD2 genes). Individuals homozygous for the risk alleles for all 3 of these SNPs are estimated to be at 20 fold higher risk (CI ~9-49) for Crohn's disease. From the largest most recent survey, the Crohn's disease-associated SNPs for IBD5 and NOD2 are, respectively, rs6...
38.3	rs2076756 (A;A)	normal

			rs2076756 is a SNP of the NOD2 gene found in a genome-wide association study to be associated with Crohn's disease. In several European populations, the minor NOD2 allele, rs2076756(G), is associated with increased risk for Crohn's disease. The odds ratio (pooled over several populations) is 1.71 (CI: 1.42-2.05, p=6x10^-8).
48.3	rs11362 (G;G)	normal risk

			Heterozygotes for SNP rs11362, located in the DEFB1 gene, are reported to be at increased risk for colonic Crohn's disease - but not the ileal or ileocolonic forms of the disease - based on a study of 190 Caucasians. The odds ratio is 2.393 (CI: 1.18-4.87, p=0.02).
51.7	rs1004819 (C;C)	common

			SNP rs1004819, in the IL23R gene, is associated with increased risk for Crohn's disease in both Jewish and non-Jewish populations. The same risk allele is also reported to increase the risk for developing ankylosing spondylitis, based on a large study of over 1,000 Caucasian patients. The odds ratio is 1.2 (p=8.8x10e-5).[PMID 17952073, PMID 18037607] significant associations with rs1004819, rs7517847, and rs11209026. Having any CARD15 variant was associated with a significant risk for CD (P < 0.0001).
53.3	rs10889677 (C;C)	1x risk for certain autoimmune diseases; 2.3x risk for Graves disease

			SNP rs10889677, in the IL23R gene, is associated with increased risk for Crohn's disease in both Jewish and non-Jewish populations. The same risk allele for this SNP has been associated with increased risk for ankylosing spondylitis in a large study of over 1,000 Caucasian patients. The odds ratio is 1.3 (p=1.3x10e-6).[PMID 17952073, PMID 18037607] In a study of 216 North American patients with Graves' disease, the C allele of rs10889677 was 2.03x overrepresented (p=1.3x10⁴), and the homozygous rs10889677(C;C) genotype was also overrepresented (2.36x; p=1.4x10^-4) in Graves ophthalmopathy patients.
55.0	rs6908425 (C;C)	1.9x risk

			rs6908425 has been reported in a large study to be associated with Crohn's disease. The risk allele (oriented to the dbSNP entry) is (C); the odds ratio associated with heterozygotes is 1.63 (CI 1.38-2.25), and for homozygotes, 1.95 (CI 1.43-2.67).
55.0	rs2201841 (T;T)	2.4x risk for Graves' disease

			SNP rs2201841, in the IL23R gene, is associated with increased risk for Crohn's disease in both Jewish and non-Jewish populations. Another study found that the 'A allele' and 'AA genotype' were significantly overrepresented in Graves' disease patients with Graves ophthalmopathy, based on 216 North American patients. The odds ratios reported were 2.04 for the allele (p=1x10^-4), and for the so-called 'AA' genotype (presumably rs2201841(T;T) when correctly oriented to the dbSNP orientation), 2.4 (p=1x10^-4).
72.9	rs17234657 (T;T)	normal

			rs17234657 has been reported in a large study to be associated with Crohn's disease. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.54 (CI 1.34-1.76), and for homozygotes, 2.32 (CI 1.59-3.39).
78.0	rs2066844 (C;C)

			rs2066844 is mentioned in as being strongly associated with Crohn's disease [omim:CROHN DISEASE, SUSCEPTIBILITY TO]
83.3	rs8111071 (A;A)	normal

			rs8111071 has been reported in a large study to be associated with Crohn's disease. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.47 (CI 1.25-1.73), and for homozygotes, 1.28 (CI 0.56-2.88).
88.1	rs11209026 (G;G)	common

			A relatively rare allele at SNP rs11209026, in the IL23R gene, appears to provide a fairly strong protective effect against the development of Crohn's disease in both Jewish and non-Jewish populations. Note that in this study the (A;A) and (A;G) genotypes were combined for statistical reasons (there were too few (A;A) individuals to study by themselves), so the risk is shown as equal for both. associated With Inflammatory Bowel Diseases but Not With Celiac Disease rs11209026 had a protective effect for IBD in the case-control analysis (odds ratio [OR] 0.19, 95% confidence interval [CI] 0.10-0.37, P= 6.6E-09). Both CD (OR 0.14, CI 0.06-0.37, P= 3.9E-07) and UC (OR 0.33, CI 0.15-0.73, P= 1.4E-03) were associated with IL23R. rs2241880 was associated with CD susceptibility (OR 1.36, CI 1.12-...
None	rs1800471 (C;C) ambig

			rs1800471 encodes a change at codon 25 of the TGFB1 gene. It is reported to predispose several organs to fibrosis, and in relation to Crohn's disease, it was associated with stricturing Crohn's disease (odds ratio 2.63, CI: 1.16-5.88, p=0.01) and a shorter time to intestinal resection (p = 0.06) in a study of several hundred Australian patients.

Depression
33.9	rs1801133 (C;T)	multiple, incl 1.17x for gastric cancer

			rs1801133 is a SNP that is relatively common and has been studied for (relatively) a long time. Also known as C677CT, Ala222Val, and A222V, it encodes a variant in the MTHFR gene, which encodes an enzyme involved in folate metabolism. Homozygous rs1801133(T;T) individuals have ~30% of the expected MTHFR enzyme activity, and rs1801133(C;T) heterozygotes have ~65% activity, compared to the most common genotype, rs1801133(C;C). This reduced activity (i.e. this SNP) has been linked at least once to each of the following disorders (though not necessarily reproducibly): coronary artery disease neural tube defects migraine thrombosis preeclampsia cleft lip/palate autism depression schizophrenia cancer, including **gastric cancer With regard to gastric cancer, a meta-analysis combining 1...
53.3	rs1360780 (C;C)	normal

			In Caucasian non-Hispanics, the rs1360780(T) allele is associated with increased risk for depression, with an odds ratio of 1.39 (CI: 1.14-1.70, p=0.046). This same SNP, which is in the FKBP5 gene, may influence how patients respond to antidepressants including citalopram. rs1360780(T;T) homozgyotes tend to report more depressive episodes, but they also respond better to treatment with antidepressants. rs9296158 rs3800373 rs1360780 rs9470080 linked with the severity of child abuse to predict level of adult PTSD symptoms after correcting for multiple testing.
55.0	rs7997012 (A;G)	normal risk

			rs7997012, located in an intron of the HTR2A gene, was found to be associated with a somewhat increased rate of successful response to treatment of depression with the drug citalopram. From this article : 'HTR2A encodes the serotonin 2A receptor, which is downregulated by citalopram. Participants who were homozygous for the A allele had an 18% reduction in absolute risk of having no response to treatment, compared with those homozygous for the other allele.' * See also [http://www.anxietyinsights.info/antipressant_effectiveness_predicted_by_gene_variation.htm Anxiety Blog] posting
63.3	rs1954787 (C;T)	normal risk

			rs1954787, located in an intron of the HTR2A gene, was found to be associated with a somewhat increased rate of successful response to treatment of depression with the drug citalopram. From the abstract of this article: 'The effect size of (this) GRIK4 marker alone was modest, but homozygote carriers of the treatment-response-associated marker alleles of both the GRIK4 and HTR2A (see rs7997012) genes were 23% less likely to experience nonresponse to (citalopram) treatment relative to participants who did not carry any of these marker alleles.' * See also [http://www.anxietyinsights.info/antipressant_effectiveness_predicted_by_gene_variation.htm Anxiety Blog] posting

Diabetes
45.8	rs237025 (C;T)	MET/VAL moderate [[diabetes]] susceptibility
			This [http://www.emaxhealth.com/23/6527.html press release] provides a helpful summary of . The paper concludes that in rs237025, the MET form increases the odds of type-1 diabetes. This form produces both MET and VAL. suggests the contribution of rs237025 to both type-1 diabetes\|type 1 and type-2 diabetes\|type 2 diabetes susceptibility.
			suggests the contribution of rs237025 to both type-1 diabetes\|type 1 and type-2 diabetes\|type 2 diabetes susceptibility. It is also known as Met55Val or A163G. This [http://www.emaxhealth.com/23/6527.html press release] provides a helpful summary of . The paper concludes that in the M55V mutation, the MET form increases the odds of type-1 diabetes. This was the first snpedia snp and has one of the largest (aka most difficult) Watson aligments.

Dyslexia
26.7	rs761100 (G;G)	higher risk for dyslexia

			The more common allele of rs761100 has been linked to increased risk for developmental dyslexia in a study of ~300 British families. While odds ratios were not reported, the significance was reported as p=0.02.
28.3	rs2143340 (C;T)	increased risk

			Rs2143340, a SNP in the TTRAP gene, is in a region that crops up in several independent studies as likely to associated with dyslexia. The risk allele in the US/UK Caucasian populations studied is (C), and it is indicative of a risk haplotype found in ~18% of the general population but up to ~28% of severely dyslexic individuals. It is not thought that rs2143340 is a functional SNP; instead, it marks the haplotype known as rs4504469-rs2038137-rs2143340 '1-1-2' since the other two SNPs are the common forms whereas the significant form for rs2143340 is the rare form. The functional effect of this haplotype appears to be on the KIAA0319 gene, in that KIAA0319 gene activity associated with the 1-1-2 risk haplotype is 40% lower than for other haplotypes, and other genes aren't noticeably affec...
38.3	rs807701 (T;T)	common

			Rs807701, a SNP in the DCDC2 gene, is in a region that crops up in several independent studies as likely to associated with dyslexia. The risk allele in the Caucasian populations studied is (A). One study reports that the odds ratio for rs807701 genotypes increases if calculated from subsets of more severely dyslexic individuals as compared to more heterogenous, larger groups of dyslexic individuals. The genotype relative risk (GRR) for rs807701(C;C) increased from 1.88 (95% CI 0.893.97; P=.058) for the larger group up to 5.04 (95% CI 1.3518.88; P=.002) for the most severely affected group. Combined with another SNP marker in the DCDC2 gene, rs793862, the (haplotype) GRR also increased for the homozygous haplotype rs793862(A)-rs807701(C), from 4.11 (95% CI 2.776.08; P<.0001) for the la...
38.6	rs4504469 (C;C)	common

			Rs4504469, a nonsynonymous SNP in exon 4 of the KIAA0319 gene, is in a region that crops up in several independent studies as likely to associated with dyslexia. The risk allele in the Caucasian populations studied is (T). The odds ratio in a study of case:control study of ~400 Caucasians associated with rs4504469(T) is 1.51 (CI: 1.171.95, p = 0.002).
None	rs793862 (G;G)	common

			Rs793862, a SNP in the DCDC2 gene, is in a region that crops up in several independent studies as likely to associated with dyslexia. The risk allele in the Caucasian populations studied is (A). One study reports that the odds ratio for rs793862 genotypes increases if calculated from subsets of more severely dyslexic individuals as compared to more heterogenous, larger groups of dyslexic individuals. The genotype relative risk (GRR) for rs793862(A;A) increased from 3.15 (95% CI 1.307.66; P=.011) for the larger group up to 5.40 (95% CI 1.2723.01; P=.002) for the most severely affected group. Combined with another SNP marker in the DCDC2 gene, rs807701, the (haplotype) GRR also increased for the homozygous haplotype A-C, from 4.11 (95% CI 2.776.08; P<.0001) for the larger group, up to 11...
None	rs3212236 (A;G)	normal risk

			The more common allele of rs3212236 has been linked to increased risk for developmental dyslexia in a study of ~300 British families. While odds ratios were not reported, the significance was reported as p=0.02.

Earwax
21.7	rs17822931 (C;T)	wet earwax

			This SNP determines wet vs dry earwax as well as sweat production it is commonly (T;T) for asians and (C;C) for europeans and africans.

Endometrial cancer
25.0	rs4680 (A;A)	multiple associations, see details

			rs4680 is a well studied SNP in the catechol-O-methyltransferase COMT gene. rs4680 is also known as the Val158Met polymorphism; note that rs4680(G) encodes the Val, considered to be the high enzymatic activity form, and rs4680(A) encodes the Met (lower enzymatic activity). Part of a three-marker haplotype rs737865-rs4680-rs165599 rs4680, a functional Val/Met polymorphism, showed modest association with Irish familial schizophrenia. Haplotype A-G-A for SNPs rs737865-rs4680-rs165599 was preferentially transmitted to the affected subjects. A study of 400 individuals reported that an increase in plasma total homocysteine (tHcy) of 10.4% (CI: 0.01-0.21, p=0.03) for associated with rs4680(A;A) homozygotes compared with rs4680(G;G) subjects. The (A;A) genotype was also more common, but statistica...
26.7	rs4633 (T;T)	higher risk for endometrial cancer

			rs4633 is a variant at codon 62 of the COMT gene, however, it does not change the amino acid sequence of the COMT protein. In a study of 150 (Caucasian) cases of endometrial cancer, a significant increase in rs4633(T;T) genotype was observed in patients compared to controls (OR = 2.39, CI: 1.31-4.37, p = 0.004). Furthemore, the frequency of the C-G haplotype of rs4633-rs4680 was significantly higher in controls (p < 0.0001) than in patients. This correlated with lower expression levels of the COMT protein in carriers of these alleles. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1180576 pubmed 1180576] Schizophrenia Susceptibility Genetic basis for individual variations in pain perception and the development of a chronic pain condition

Eosinophilic esophagitis
63.3	rs2302009 (T;T)	normal

			rs2302009 is a SNP located in the 3' untranslated region of the CCL26 gene. This gene (and this SNP) were discovered to be strongly associated with 117 patients with eosinophilic esophagitis, a form of esophagitis (or inflammation of the esophagus) that shares many symptoms with gastroesophageal reflux disease (GERD). rs2302009(G) is the risk allele. The rs2302009(G;G) homozygous genotype is the most predisposed to developing eosinophilic esophagitis (odds ratio 4.55, CI 1.7112.39). The heterozgyote (rs2302009(G;T)) genotype's risk was indistinguishable statistically from the normal rs23020099(T;T) genotype. [omim:ESOPHAGITIS, EOSINOPHILIC, SUSCEPTIBILITY TO]

Eye color
61.7	rs12913832 (G;G)	blue eye color, 99% of the time

			rs12913832 is a SNP near the OCA2 gene that may be functionally linked to blue or brown eye color, due to a lowering of promoter activity of the OCA2 gene. Blue eye color is associated with the rs12913832(G;G) genotype.[PMID 18172690, PMID 18252222] rs12913832 is also part of a haplotype spanning 166kB on chromosome 15, defined by 13 SNPs listed below, that is found in 97% of all Caucasians with blue eyes. In this haplotype, variations in rs1129038 and rs12913832 are relatively common in Caucasians though rare among other ethnic groups. The 'h-1' haplotype found in homozygous state in 97% of individuals with blue eye color is composed as follows : rs4778241(C) rs1129038(A) rs12593929(A) rs12913832(G) rs7183877(C) rs3935591(G) rs7170852(A) rs2238289(T) rs3940...
78.0	rs7495174 (A;A)	blue/gray eyes more likely

			rs7495174 is located in intron 1 of the OCA2 gene. The (A) allele (in dbSNP orientation) is associated with blue or green eye color in Caucasians. . This SNP is 1 of 3 SNPs defining a haplotype that has been studied for association with eye color. The full details on the correspondence between the haplotype and eye color can be found on the OCA2 page.

Gastric cancer
33.9	rs1801133 (C;T)	multiple, incl 1.17x for gastric cancer

			rs1801133 is a SNP that is relatively common and has been studied for (relatively) a long time. Also known as C677CT, Ala222Val, and A222V, it encodes a variant in the MTHFR gene, which encodes an enzyme involved in folate metabolism. Homozygous rs1801133(T;T) individuals have ~30% of the expected MTHFR enzyme activity, and rs1801133(C;T) heterozygotes have ~65% activity, compared to the most common genotype, rs1801133(C;C). This reduced activity (i.e. this SNP) has been linked at least once to each of the following disorders (though not necessarily reproducibly): coronary artery disease neural tube defects migraine thrombosis preeclampsia cleft lip/palate autism depression schizophrenia cancer, including **gastric cancer With regard to gastric cancer, a meta-analysis combining 1...

Glaucoma
None	rs28936694 (C;C)

		[omim:GLAUCOMA 1, OPEN ANGLE, A, DIGENIC]

Heart disease
3.3	rs662799 (A;G)

			this snp prevents [http://www.medicalnewstoday.com/medicalnews.php?newsid=67543 weight gain from high fat diets]. rs662799 -1131T>C in APOA5 is present in approximately 13% of this population, modulates the effect of fat intake on BMI and obesity risk in both men and women.
13.3	rs2713604 (A;G)

			[http://genetics.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pgen.0020139 This paper] implicates this snp as playing a role in heart disease. Having a C at this position is considered normal. Having a T at this position increases the risk of heart disease. Approximate 27% of people carry this risky form.
13.6	rs17576 (G;G)	higher risk for lung cancer, and, COPD in smokers; normal risk for MI

			rs17576, also known as Gln279Arg or Q279R, is a SNP in exon 6 of the matrix metalloproteinase-9 MMP9 gene. The rs17576(G) allele encodes the Arg (R). In a study of 385 male veterans with greater than 20 pack-years of cigarette smoking, rs17576(G) allele carriers were at higher risk for chronic obstructive pulmonary disease (COPD). The rs17576(G;G) homozygous genotype was at 3-fold increased risk for COPD. A study of 744 Chinese patients with lung cancer found that the rs17576(G;G) genotype was associated with higher risk of lung cancer with metastasis (adjusted OR, 1.79, CI: 1.03-3.08) compared to the (A;A) genotype. rs17576 is also one of two SNPs in the MMP9 gene associated with increased risk for myocardial infarction, but not coronary artery disease. The relatively weak odds ratios for...
32.2	rs788016 (A;A)

			G-C-T-C haplotype of rs2340690-rs788016-rs2305560-rs2565163 has odds ratio of 1.91 (CI: 1.26-2.89, p=0.002) for coronary heart disease compared to G-T-T-C, based on a study of 1,000 Han Chinese patients and matched controls. * Note: Haplotype allele assignments may not be in dbSNP orientation.
60.0	rs3803 (C;C)

			Category:needs help Category:interesting [http://genetics.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pgen.0020139 This paper] implicates this snp as playing a role in heart disease. Having a G at this position is considered normal. Having an A at this position reduces the risk of heart disease. Approximate 15% of all people carry this allele. '''Technical note:''' This applies to many other snps, but here is the first clean case I've encountered. dbsnp shows ss3839 and ss16241517 are being read 'fwd' ss16940640 and ss44449258 are being read in 'rev'. This has C/T alleles when read forward, and A/G when read in reverse. Since the authors of the paper above describe this as an A/G snp, it seems they are reading in reverse. Often papers include even less information, ...
61.7	rs8055236 (G;G)	2.2x risk
			2.2x higher risk for heart disease
			rs8055236 has been reported in a large study to be associated with heart disease, in particular, coronary artery disease. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.91 (CI 1.33-2.74), and for homozygotes, 2.23 (CI 1.56-3.17).
88.3	rs3135506 (G;G) ambig

			no known effect also known as S19W discussed in , however the snp which prevents [http://www.medicalnewstoday.com/medicalnews.php?newsid=67543 weight gain from high fat diets] is rs662799
None	rs1800787 (C;C)

			rs1800787(T;T) homozygotes are at 6 fold higher risk compared to (C;C) homozygotes or (C;T) heterozygotes for carotid atherosclerosis . This polymorphism is known as the 'C148-T' variant, and is located in at the '-148' position of the FGB gene, also known as beta fibrinogen. Note: due to inconsistencies between databases and the literature, the association of this rs# with this polymorphism name as published is highly likely but not guaranteed.

Hemochromatosis
91.7	rs1800562 (G;G)	Normal/Common

			rs1800562 represents a SNP that accounts for ~85% of all cases of hemochromatosis, a disorder who's symptoms include cirrhosis of the liver, diabetes, hypermelanotic pigmentation of the skin, and heart failure. [http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=235200 OMIM] indicates that liver cancer is responsible for about one-third of deaths of rs1800562(A;A) homozygotes, and since hemochromatosis is a relatively easily treated disorder if diagnosed, this is a form of preventable cancer. The rs1800562(A) allele is known as the C282Y mutation, and it is found at a frequency of around 5-10% in many Caucasian populations, leading to an incidence of (A;A) homozygotes around 1 in 200. Early identification of rs1800562(A;A) homozygotes can prevent complications of hemochromatosis; however, ...

High blood pressure
36.7	rs1801253 (C;G) ambig	depends on [[rs1801252]]

			Variation at this SNP, located in the ADRB1 gene, may encode either the amino acid glycine or arginine at amino acid position 389 of the corresponding protein, the beta-1 adrenergic receptor. This protein is the target of beta blocker drugs, and so how well the drug works to help lower a patients high blood pressure depends in part on this SNP. The status of this SNP is often reported together with the status of SNP rs1801252, which encodes an amino acid variant at position 49 of the same (ADRB1) protein. One of the best known studies of the effects of these 2 separate SNPs on the average efficacy of the beta blocker metoprolol in lowering blood pressure (BP) can be summarized for patients with the corresponding genotypes as follows : *rs1801252(A;A) and rs1801253(C;C) carriers: 15 point d...
38.3	rs4149601 (G;G)

			rs4149601 has been associated with hypertension. This SNP by itself was associated with diastolic blood pressure (DBP) (p=0.03) and DBP progression over time (p=0.04); in genotypic combination with intronic NEDD4L SNP rs2288774 it was associated with systolic blood pressure (SBP) (p=0.01), DBP (p=0.04), and progression of both SBP (p=0.03) and DBP (p=0.05) over time.
43.3	rs3755351 (C;C)	>1.3x risk for hypertension

			rs3755351, a SNP in the ADD2 gene, was associated with risk for hypertension in a study involving 1,500+ Japanese patients. The odds ratio associated with the risk allele, rs3755351(C), which is also the most common allele, is 1.30 (CI: 1.15 - 1.46, p = 0.00002). Note that a neighboring ADD2 SNP in close (r2 of 0.806) proximity, rs17006246, was associated with hypertension in a diabetes study ; however, in this case, it was in 'the opposite direction of effect'. This discrepancy has not been resolved.
48.3	rs9739493 (C;T)	higher risk for hypertension

			rs9739493, a SNP in the KIAA0789 gene, was associated with risk for hypertension in a study involving 1,500+ Japanese patients. The odds ratio associated with the risk allele, rs9739493(T), was not directly reported. Note that another SNP in the KIAA0789 gene, rs3794260, was determined to be in a different linkage disequilibrium block, and is thus thought to be an independent risk factor for hypertension.
61.7	rs4961 (G;G)	normal

			rs4961 is a variation in the adducin 1 ADD1 gene, encoding a change from a glycine to a tryptophan, so it is also known as G460W. Originally, a study of 477 Italian patients indicated that carriers of one or two rs4961(T) alleles were at 1.8x increased risk for hypertension (CI: 1.32-2.43). This study also indicated that carriers of the risk (T) allele responded better to diuretics and sodium-restricted diets, in that they tended to lower their blood pressure by ~10 mmHg points compared to rs4961(G;G) homozygotes similarly treated. Subsequent studies have tended to confirm this association, and to extend it to risk for heart disease. They also have tended to confirm that risk allele carriers respond better to therapy. In a study of ~2200 Belgian patients, rs4961(T) carriers were generally ...
None	rs5186 (A;A)	normal risk

			rs5186 is a SNP known as +1166A/C, located in the 3' untranslated region of the angiotensin II receptor type 1 gene AGTR1, which is also known as AT2R1 or AT1R. It is among the most studied of over 50 SNPs in AGTR1. The rs5186(C) allele is associated with increased risk for essential hypertension in Caucasian populations with an odds ratio of 7.3 (homozygote (C;C) compared to (A;C) and (A;A), CI: 1.9-31.9,p=0.0015).[PMID 8021009, PMID 9084931] There are likely to be ethnic differences in risk; while the rs5186(C) allele was associated with hypertension in a Chinese population , it was not been observed as a risk in a Japanese population. Age and gender may also influence risk, as discussed in a review of AGTR1 SNPs and their role in hypertension and related disorders. Pregnant women who ar...

Hirschsprung
None	rs2435357 (C;C)

		This SNP, located in the first intron of the RET gene, has been associated with Hirschsprung disease. The risk allele (in dbSNP orientation) is rs2435357(A), with greater affect in males.

Intrahepatic cholestasis of pregnancy
40.0	rs3740066 (G;G)	average

			rs3740066, a SNP in the ABCC2 gene, is reported to be associated with a higher risk of developing intrahepatic cholestasis of pregnancy (ICP) based on a study of ~70 Argentinian patients. ICP is associated with increased fetal risks such as premature birth or intrauterine death. The risk allele is rs3740066(A), and the odds ratio for homozygous rs3740066(A;A) mothers is 4.44 (CI: 1.83 - 10.78), and for heterozygous mothers 1.65 (CI: 0.76 - 3.64), compared to rs3740066(G;G) mothers.

Lactose intolerance
39.0	rs4988235 (C;T)	can digest milk

			Also known as 'C/T(-13910)', and located in the MCM6 gene but with influence on the lactase LCT gene, rs4988235 is one of two SNPs that is associated with the primary haplotype associated with hypolactasia, more commonly known as lactose intolerance in European Caucasian populations. , In these populations, the rs4988235(T) allele is both the more common allele and the one associated with lactase persistence; individuals who are rs4988235(C;C) are likely to be lactose intolerant. In populations of sub-Saharan Africans, though, the rs4988235(T) allele is so rare that it's unlikely to be predictive of lactase persistence, and other SNPs are predictive instead. [PMID 15106124, PMID 17159977] * See also [http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=601806&a=601806_AllelicVariant0001 OMIM...
None	rs182549 (C;T)

			Also known as 'G/A(-22018)' and located in the MCM6 but with influence on the lactase LCT gene, rs182549 is one of two SNPs that is associated with the primary haplotype associated with hypolactasia, more commonly known as lactose intolerance in European Caucasian populations. [PMID 11788828, PMID 15114531] In these populations, the rs182549(C) allele (as named in accordance with dbSNP) is both the more common allele and the one associated with lactose intolerance. In populations of sub-Saharan Africans, though, the rs182549(C) allele is unlikely to be predictive of lactose intolerance, and other SNPs are predictive instead. [PMID 15106124, PMID 17159977] * See also [http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=601806&a=601806_AllelicVariant0002 OMIM 601806.0002]

Longevity
23.3	rs1800795 (G;G) ambig	more IL6; certain risks, see details
			rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. In the literature, it is almost universally referred to as the IL6 '-174' polymorphism. It tends to be quite polymorphic in Caucasians, but Asian and African populations are almost monomorphic (for the (G) allele). The rs1800795(G) allele, generally associated with higher levels of IL6, has been associated with increased risk in the following studies: * The rs1800795(G) allele was significantly associated with type-2 diabetes (odds ratio 1.51, CI: 1.11-2.07, p=0.0096) in a study of 700 elderly Caucasians. * Following a kidney transplant, patients with rs1800795(G;G) genotypes have a higher risk of new-onset diabetes an...
			rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. In the literature, it is almost universally referred to as the IL6 '-174' polymorphism. It tends to be quite polymorphic in Caucasians, but Asian and African populations are almost monomorphic (for the (G) allele). It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. Studies on rs1800795 now include potential associations with heart disease, Kaposi's sarcoma, type-2 diabetes, stroke, obesity, Hodgkin's lymphoma, sudden ...
51.7	rs5882 (A;A)

			[omim:LONGEVITY, EXCEPTIONAL]
61.7	rs1042522 (G;G) ambig	(?)longer lifespan?

			This SNP, a variant in the TP53 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (C). The minor allele encodes an arginine at position 72 of the protein (where there's normally a proline), and the SNP is commonly called the Arg72 variant, although P72R is also common in the literature. Minor allele homozygotes, i.e. rs1042522(C;C) genotypes, live on average 3 years longer than major allele (G;G) homozygotes, based on a study of 9,200+ Danish individuals. The increased longevity is speculate...
80.0	rs2811712 (A;A)	normal risk

			rs2811712 is a SNP associated with physical function in older individuals, and thus indirectly associated with longevity. In a study ultimately totaling over 3,300 elderly Caucasian individuals, the less common rs2811712(G) allele was associated with reduced physical impairment. Overall, severely limited physical function was present in 15.0% of the more common rs2811712(A;A) homozygotes, versus 7.0% of the rs2811712(G;G) homozygotes, yielding a per risk allele odds ratio of 1.48 (CI: 1.17-1.88, p=0.001).

Lumbar disc disease
55.0	rs2073711 (C;C)	higher risk of LDD

			A study of Asian patients with lumbar disc disease (LDD) implicates each copy of a (C) allele of SNP rs2073711 (as oriented with respect to dbSNP) as increasing risk about 1.6 fold. [omim:LUMBAR DISC DISEASE, SUSCEPTIBILITY TO]
73.3	rs1676486 (G;G)	average

			Lumbar disc herniation (LDH), a form of lumbar disc disease, is one of the most common musculoskeletal diseases. rs1676486, a SNP also known as c.4603C-->T in the COLL11A1 gene (one of 3 Type XI collagen genes), has been implicated in a study of ~800 Japanese patients as being associated with LDH. The risk allele in dbSNP orientation is (A), and the odds ratio associated with the allele is 1.42 (CI: 1.23 - 1.65).

Lung cancer
13.6	rs17576 (G;G)	higher risk for lung cancer, and, COPD in smokers; normal risk for MI

			rs17576, also known as Gln279Arg or Q279R, is a SNP in exon 6 of the matrix metalloproteinase-9 MMP9 gene. The rs17576(G) allele encodes the Arg (R). In a study of 385 male veterans with greater than 20 pack-years of cigarette smoking, rs17576(G) allele carriers were at higher risk for chronic obstructive pulmonary disease (COPD). The rs17576(G;G) homozygous genotype was at 3-fold increased risk for COPD. A study of 744 Chinese patients with lung cancer found that the rs17576(G;G) genotype was associated with higher risk of lung cancer with metastasis (adjusted OR, 1.79, CI: 1.03-3.08) compared to the (A;A) genotype. rs17576 is also one of two SNPs in the MMP9 gene associated with increased risk for myocardial infarction, but not coronary artery disease. The relatively weak odds ratios for...
53.3	rs10508266 (G;G)

			rs10508266 and rs3750861 near KLF6 shows significant association with Lung cancer risk.
85.0	rs3750861 (C;C)

			rs10508266 and rs3750861 shows significant association with lung cancer risk rs3750861 affects expression of KLF6 splicing variants in prostate cancer and we found that its rare allele is associated with reduced lung cancer risk
90.0	rs2250889 (C;C) ambig	1.69x higher risk for lung cancer

			rs2250889, a SNP also known as P574R, is located in the MMP9 gene. In a study of 744 Chinese patients with incident lung cancer rs2250889(C;G) heterozygotes and rs2250889(C;C) homozygotes had 1.46-fold (CI: 0.94-2.26) and 1.69-fold elevated risk (CI: 1.10-2.60) for lung cancer, respectively, compared with the (G;G) genotype. There was an additive effect of having additional MMP9 risk alleles.
98.3	rs2308327 (A;A)	normal

			rs2308327, also known as K178R, is a SNP in the MGMT gene. The more common allele, rs2308327(A), encodes a lysine (K) at codon 178, while the (G) allele encodes an arginine (R). In a pooled analysis of 200+ lung cancer patients, the rs2308327(G) allele was reported to provide a protective effect against lung cancer, and furthermore, more (G) alleles meant more protection, particularly for smokers. The odds ratios reported (p=0.003) were 0.67 (CI: 0.45-1.01) for heterozygotes, and 0.10 (CI: 0.01-0.94) for rs2308327(G;G) homozygotes. In a study of 300+ colon cancer cases, rs2308327(G), in linkage disequilibrium with the previously reported MGMT Ile(143)Val SNP, had an inverse association with colorectal cancer risk (odds ratio 0.52, CI: 0.35-0.78, unadjusted p(trend) = 0.0003 for the additiv...

Lupus
21.7	rs11574637 (C;T)

			Associated with systemic lupus erythematosus (SLE)
23.3	rs509749 (A;A)	common; slight increase in SLE risk

			rs509749 is a SNP in exon 8 of the LY9 gene; this SNP is also known as Met602Val. The (A) allele encodes the Met; the (G) allele encodes the Val. The rarer (G) allele is undertransmitted in a family-based association study of systemic lupus erythematosus, leading to the conclusion that the (A) allele increases risk for SLE by increasing cytokine production and thereby enhancing the immune response.
28.3	rs1800630 (A;C)	1.8x increased lupus risk

			rs1800630 is a SNP upstream of the tumor necrosis alpha (TNF) gene; this SNP is also typically called the -863 variant. In a study of 154 Thai patients with systemic lupus erythematosus (SLE), rs1800630(A) allele frequency was significantly increased, with an odds ratio of 1.85 (CI: 1.21-2.83, p(corr) = 0.009). This allele was also found to be significantly increased in the SLE group with Raynaud's phenomenon compared to SLE without Raynaud's phenomenon ( odds ratio of 2.23, CI: 1.21-4.10, p(corr) = 0.048).
30.0	rs3748079 (A;G)	normal risk

			rs3748079 is a SNP in the promoter region of the ITPR3 gene; it is also known as -1990C>T. rs3748079 has been linked to increased risk for systemic lupus erythematosus (SLE) in two independent Japanese case-control samples (p=0.0000000178 with odds ratio of 1.88, CI:1.51-2.35). Individuals with risk genotypes of both rs3748079 and rs3095870, in the ITPR3 and NKX2.5 genes, respectively, have even high risk for SLE (odds ratio 5.77). This particular SNP also revealed associations with rheumatoid arthritis (RA) (p=0.0084 with odds ratio of 1.23, CI:1.05-1.43) and with Graves' disease (GD) (p=0.00036 with odds ratio of 1.57, CI:1.22-2.02). Note that the orientation of this SNP as published is reversed compared to the dbSNP entry.
36.7	rs10516487 (C;T)

			rs17266594 rs10516487 rs3733197 gene associated with systemic lupus erythematosus.
46.7	rs1205 (C;T)

			Although somewhat lacking in statistical power, several reports have linked rs1205, a synonymous mutation known as CRP4 in the C-reactive protein CRP to the autoimmune disorder SLE, systemic lupus erythematosus. The risk allele in dbSNP orientation is (T). [PMID 14645206, PMID 15897982] [omim:C-REACTIVE PROTEIN, PENTRAXIN-RELATED; CRP]
52.5	rs13277113 (G;G)

			Associated with systemic lupus erythematosus (SLE)
81.7	rs2187668 (G;G)	average

			In at least UK populations, and perhaps others, SNP rs2187668 is a tag SNP for the HLA-DRB10301 allele. The HLA-DRB10301 allele is the allele presenting the highest risk for developing lupus, and it appears to act in a dominant manner (i.e. inheriting 2 copies is no worse than inheriting 1 copy). In dbSNP orientation, the risk allele is rs2187668(A), with an odds ratio of 2.3x (CI: 1.7 - 3.2, permuted p < 0.0001). From individuals with the most common rs2187668](G;G) genotype, risk is reduced for celiac disease, with an odds ratio of 0.30x according to a study of ~800 patients.

Migraines
26.7	rs5443 (C;C)	average

			rs5443, a SNP in the G-protein beta3 subunit (GNB3) gene that is more commonly known as the C825T variant, has been linked to a number of metabolic conditions including obesity, coronary artery disease, insulin resistance and therefore diabetes, left ventricular hypertrophy, and hypertension. It has also been linked to how well a patient responds to Viagra (sildenafil). Several studies have been unable to replicate one or more of the associations in at least some populations between this SNP and these conditions. The more notable studies include: rs5443(T) allele carriers are 2-3 fold more likely to be obese in Caucasian, Chinese, and African American populations. rs5443(T) carriers are clearly at higher risk for hypertension, but this review indicates that whether they are also at incr...
28.3	rs1042838 (G;T)	1.26x risk for ovarian cancer

			Two SNPs in haplotype block 4 of the PGR gene were associated with an increased risk of ovarian cancer among homozygous carriers as compared with noncarriers: rs1042838 (PROGINS allele; odds ratio [OR] = 3.23, 95% confidence interval [CI] = 1.19 to 8.75, P = .022) and rs608995 (minor allele; OR = 3.10, 95% CI = 1.63 to 5.89, P<.001). For rs1042838, the risk allele in orientation to the corresponding dbSNP entry is (T). This SNP, which is located in the progesterone receptor gene PGR, has also been reported to be associated with migraine-associated vertigo. SNPs in genes involved in female hormonal pathways have been a subject of particular interest in the study of migraines because females appear to be more prone to migraines than males.

Multiple sclerosis
42.4	rs6604026 (C;T)	1.15x risk

			rs6604026 has been reported in a large study to be associated with multiple sclerosis. The risk allele (oriented to the dbSNP entry) is (C); the odds ratio associated with this allele is 1.15 (CI 1.08-1.22).
43.3	rs4763655 (G;G)	common

			rs4763655 has been reported in a large study to be associated with multiple sclerosis. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with this allele is 1.10 (CI 1.04-1.17).
56.7	rs6897932 (C;C)	increased risk multiple sclerosis

			The (C) allele of rs6897932, located in the alternatively spliced exon 6 of IL7RA gene and encoding the amino acid threonine rather than isoleucine at amino acid position 244, is associated with a slight increase (18%) in risk of developing multiple sclerosis. [PMID 17660817; Nature Genetics 39, 1083 - 1091 (2007) SG Gregory et al.] Note that the (C) allele is the most common at this position in all known populations and influences the ratios of the alternative isoforms (membrane bound and soluble) of the gene. [http://thegenesherpa.blogspot.com/2007/07/ms-genes-and-gwas.html blog post] giving perspective on the significance of this snp a significant risk factor for multiple sclerosis in four independent (overall P = 2.9 x 10(-7)) influences the amount of soluble and membrane-bound isofor...
56.7	rs3135388 (C;C)

			Source [http://www.nature.com/ng/journal/v38/n10/fig_tab/ng1885_T1.html nature] rs3135388 is highly (> 99%) correlated with the HLA-DRB11501 allele, and it's risk allele (T) is associated with a 3 to 6 fold higher risk for developing multiple sclerosis. It has also been associated with other autoimmune diseases, such as SLE. Note that the HLA-DRB11501 allele is fairly common; for example, it occurs in 15-30% of most individuals of Northern European origin.
100.0	rs870849 (C;T)

			rs870849, a SNP in the LAG3 gene, has been associated with multiple sclerosis.

Neuroblastoma
10.0	rs9295536 (A;A)	2x increased risk for neuroblastoma

			SNPs clustered in one region of chromosome 6p22 have been linked to increased risk for the exceedingly rare childhood cancer known as neuroblastoma. A study involving 720 patients determined that rs9295536(A;A) genotypes had increased likelihood of neuroblastoma development (odds ratio 1.93, CI: 1.55 to 2.40, p=8 x 10^-8). At-risk homozygotes diagnosed with neuroblastoma had, on average, more malignant clinical presentation, more aggressive disease, and poorer long-term survival. For more information on this cluster of SNPs, see rs6939340.
13.8	rs4712653 (C;C)	2x increased risk for neuroblastoma

			SNPs clustered in one region of chromosome 6p22 have been linked to increased risk for the exceedingly rare childhood cancer known as neuroblastoma. A study involving 720 patients determined that rs4712653(C;C) genotypes had increased likelihood of neuroblastoma development (odds ratio 1.96, CI: 1.57 to 2.43, p=7 x 10^-8). At-risk homozygotes diagnosed with neuroblastoma had, on average, more malignant clinical presentation, more aggressive disease, and poorer long-term survival. For more information on this cluster of SNPs, see rs6939340.
15.0	rs6939340 (G;G)	2x increased risk for neuroblastoma

			SNPs clustered in one region of chromosome 6p22 have been linked to increased risk for the exceedingly rare childhood cancer known as neuroblastoma. A study involving 720 patients determined that rs6939340(G;G) genotypes had increased likelihood of neuroblastoma development (odds ratio 1.97, CI: 1.58 to 2.45, p=9.3 x 10^-15). At-risk homozygotes diagnosed with neuroblastoma had, on average, more malignant clinical presentation, more aggressive disease, and poorer long-term survival. Presumably driven primarily by the at-risk homozygotes, the rs6939340(G) allele was considered to be a risk factor, however, there was insufficient data to conclude whether rs6939340(A;G) heterozygotes were actually at any increased risk compared to rs6939340(A;A) 'wild-type' homozygotes. Note that th...

Nicotine dependence
20.0	rs9217 (G;G)

			Variations in this snp have been linked to nicotine dependence [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16874522&query_hl=3&itool=pubmed_docsum]
38.3	rs1051730 (C;C)	normal

			rs1051730, also known as D398N, is a SNP in the nicotinic acetylcholine receptor alpha 3 subunit CHRNA3 gene. In two recent (2008) studies, together comprising over 6,000 lung cancer patients of European ancestry, the rs1051730(T) allele was very significiantly associated with increased risk. Having one copy (i.e. being a rs1051730(C;T) genotype) increased risk for lung cancer about 1.3x, and having two copies (rs1051730(T;T) individuals) represented 1.8x increased risk. Up to 14% of lung cancer incidence may be attributable to this allele.[PMID 18385738, PMID 18385676] An independent study published at the same time concluded that (T) allele carriers for SNP rs1051730 are not at higher risk of becoming smokers compared to (C) carriers. However, if they do smoke, (T) carriers are quite lik...
61.7	rs2302762 (C;C)
			This is the genotype of User:Watson
			Variations in this snp have been linked to nicotine dependence
76.7	rs2302765 (A;A)

			Variations in this snp have been linked to nicotine dependence [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16874522&query_hl=3&itool=pubmed_docsum]
76.7	rs2302763 (T;T)

			Variations in this snp have been linked to nicotine dependence

Non-Hodgkin Lymphoma
0.0	rs2072797 (C;C)

			rs2072797, a SNP in the UNC84B gene also known as G671S, is associated with risk for developing Non-Hodgkin Lymphoma based on a study of 458 patients. The odds ratio is 1.50 (CI: 1.12-2.00, p<0.01).
38.3	rs36686 (A;G)

			rs36686, a SNP in the B3GNT3 gene also known as H328R, is associated with reduced risk for developing Non-Hodgkin Lymphoma based on a study of 458 patients. The odds ratio is 0.74 (CI: 0.59-0.93, p<0.01).
70.0	rs5918 (T;T)	average

			The 'A2' allele of the platelet specific alloantigen system is encoded by rs5918(C), and it has been implicated as increasing the risk of myocardial infarctions, heart disease, and resistance to blood-thinning benefits of aspirin. On it's own, the A2 allele is implicated especially in early onset heart disease ; in combination with the 4G allele of the PAI1 gene, rs1799889, the increased risk of myocardial infarction in a Finnish study population was 4 fold higher (odds ratio = 4.5, p=0.001), particularly in males (odds ratio = 6.4, p=0.0005) . A2 allele carriers also appear to be relatively resistant to the anti-thrombotic (i.e. anti-clotting) actions normally associated with aspirin use. A protective effect of rs5918 has also been observed for the development of Non-Hodgkin Lymphoma, bot...
83.3	rs3132453 (C;C)

			rs3132453, a SNP in the BAT2 gene also known as V1883L, is associated with reduced risk for developing Non-Hodgkin Lymphoma based on a study of 458 patients. The odds ratio is 0.64 (CI: 0.45-0.90, p<0.01).

Obesity
3.3	rs662799 (A;G)

			this snp prevents [http://www.medicalnewstoday.com/medicalnews.php?newsid=67543 weight gain from high fat diets]. rs662799 -1131T>C in APOA5 is present in approximately 13% of this population, modulates the effect of fat intake on BMI and obesity risk in both men and women.
36.7	rs6971091 (A;G)	>2x increased risk for familial obesity

			rs6971091 is a SNP on chromosome 7 that has been linked to obesity. In a study of 400+ patients, rs6971091(A) allele carriers had an odds ratio of at least 2 for obesity defined by both body mass index (BMI) and leptin levels.
88.3	rs1528133 (A;A)	normal risk

			rs1528133, a SNP in the TUB gene, was found in a study of 492 unrelated type-2 diabetes patients to have a significant effect on body mass index and thus obesity (1.54 kg/m(2), p= 0.006). When two populations were combined, totaling ~1200 patients, the risk allele (rs1528133(C) averaged an increase of 0.54 kg/m2 (CI: 0.19-1.26). Two additional TUB SNPs, rs2272382, and rs2272383, mapping to the 3' end of the gene showed similar associations and were in linkage disequilibrium with rs1528133. A follow-up study of 1,680 middle-aged Dutch women found that this allele, rs1528133(C), was significantly associated with increased weight (+1.88 kg, p=0.022) and body mass index (+0.56 units, p= 0.05). rs1528133(C) carriers were also associated with an increased glycemic load of 1.85 units compared wi...
96.7	rs2229616 (G;G)	normal

			rs2229616, a variant in the MC4R gene known as V103I, has been associated with appetite regulation, body mass index (and thus obesity), and other features of metabolic syndrome. The most common allele is rs2229616(G); the rarer (A) allele encodes the 103I (isoleucine), and this (A) allele has been associated in a study of 8,000+ Caucasians with a significantly decreased waist circumference (1.46 cm, p = 0.020), decreased glycosylated hemoglobin (HbA1c) (0.09%, p = 0.040), and increased HDL-cholesterol (HDL-C) (+1.76 mg/dl, P = 0.056), but no change in blood pressure. The odds of having three or more components of the metabolic syndrome were substantially reduced among carriers of an rs2229616(A) allele (odds ratio = 0.46, p = 0.003). Basically, rs2229616(A) carriers are on average slight...
100.0	rs16964465 (A;A)

			rs16964465 rs16964476 may influence the risk of obesity through possible regulation of hypothalamic neuropeptide secretion
100.0	rs16964476 (A;A)

			rs16964465 rs16964476 may influence the risk of obesity through possible regulation of hypothalamic neuropeptide secretion

Osteoarthritis
0.0	rs7775 (G;G) ambig

		rs7775 (R324G) osteoarthritis at multiple joints (p = 0.07), particularly in the hip in women associated with osteoarthritis of the hip in females This is an arg324-to-gly (R324G) substitution [omim:OSTEOARTHRITIS OF HIP, FEMALE-SPECIFIC, SUSCEPTIBILITY TO]

Osteoporosis
78.0	rs3736228 (C;C)	normal

			rs3736228 is a SNP in the LRP5 gene that is also known as Ala1330Val; the more common (C) allele encodes the Ala (alanine), while the rarer (T) allele encodes the Val (valine), which is the risk allele. rs3736228(T) is associated with vertebral fractures and reduced bone mineral density (BMD), with an overall odds ratio for fractures of 1.06 per allele (CI: 1.01-1.12; 7802 fractures among 31,199 individuals studied). More specifically, the rs3736228(T) allele was associated with reduced lumbar spine BMD (p = 2.6 x 10^-9), and femoral neck BMD (p = 5.0 x 10^-6). Note that rs4988321, another LRP5 SNP (also known as Val667Met), was independently associated with BMD in this same study. [http://www.medpagetoday.com/Endocrinology/Osteoporosis/tb/9271 news] rs3736228 was assoc...
81.7	rs3770748 (T;T)	average risk?

			rs3770748, a SNP in an intron of the QPCT gene, was studied in a population of ~200 Chinese osteoporosis patients. Heterozygotes appeared to be at higher risk than either homozygote, and the association was statistically strongest in post-menopausal women.
95.0	rs4988321 (G;G)	normal

			rs4988321 is a SNP in the LRP5 gene that is also known as Val667Met; the more common (G) allele encodes the Val (valine), while the rarer (A) allele encodes the Met (methionine), which is the risk allele. rs4988321(A) is associated with vertebral fractures and reduced bone mineral density (BMD), with an overall odds ratio for vertebral fractures of 1.26 per allele (CI: 1.08-1.47; 2001 fractures among 20,488 individuals studied). More specifically, the rs4988321(A) allele was associated with reduced lumbar spine BMD density (p = 3.3 x 10^-8), and femoral neck BMD (p = 3.8 x 10^-5). Note that rs3736228, another LRP5 SNP (also known as Ala1330Val), was independently associated with BMD in this same study. triallelic and on a chip [omim:OSTEOPOROSIS-PSEUDOGLIOMA SYNDROME]

Otitis
23.3	rs1800795 (G;G) ambig	more IL6; certain risks, see details
			rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. In the literature, it is almost universally referred to as the IL6 '-174' polymorphism. It tends to be quite polymorphic in Caucasians, but Asian and African populations are almost monomorphic (for the (G) allele). The rs1800795(G) allele, generally associated with higher levels of IL6, has been associated with increased risk in the following studies: * The rs1800795(G) allele was significantly associated with type-2 diabetes (odds ratio 1.51, CI: 1.11-2.07, p=0.0096) in a study of 700 elderly Caucasians. * Following a kidney transplant, patients with rs1800795(G;G) genotypes have a higher risk of new-onset diabetes an...
			rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. In the literature, it is almost universally referred to as the IL6 '-174' polymorphism. It tends to be quite polymorphic in Caucasians, but Asian and African populations are almost monomorphic (for the (G) allele). It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. Studies on rs1800795 now include potential associations with heart disease, Kaposi's sarcoma, type-2 diabetes, stroke, obesity, Hodgkin's lymphoma, sudden ...
98.3	rs1800750 (G;G)	higher acute otitis risk

			rs1800750, a SNP located at position -376 of the TNF gene, has been linked to increased risk for recurrent acute otitis in a study of 348 children. The (adjusted) odds ratio is 3.06 for (G;G) genotypes (p=0.07).

Ovarian cancer
28.3	rs1042838 (G;T)	1.26x risk for ovarian cancer

			Two SNPs in haplotype block 4 of the PGR gene were associated with an increased risk of ovarian cancer among homozygous carriers as compared with noncarriers: rs1042838 (PROGINS allele; odds ratio [OR] = 3.23, 95% confidence interval [CI] = 1.19 to 8.75, P = .022) and rs608995 (minor allele; OR = 3.10, 95% CI = 1.63 to 5.89, P<.001). For rs1042838, the risk allele in orientation to the corresponding dbSNP entry is (T). This SNP, which is located in the progesterone receptor gene PGR, has also been reported to be associated with migraine-associated vertigo. SNPs in genes involved in female hormonal pathways have been a subject of particular interest in the study of migraines because females appear to be more prone to migraines than males.
31.7	rs523349 (C;G) ambig	increased ovarian cancer risk

			rs523349 is a SNP in the steroid-5-alpha-reductase SRD5A2 gene; it is also known as V89L. In a study of a total of 1,466 Caucasian cases of ovarian cancer, the rs523349(G) allele showed a significant trend of increasing risk of ovarian cancer per rare allele (p = 0.00002). showed '''no association''' with ovarian cancer risk 4,624 invasive epithelial ovarian cancer cases and 8,113 controls of white non-Hispanic origin ovarian cancer
83.3	rs3218536 (G;G)	normal risk

			rs3218536, a relatively rare SNP also known as Arg188His located in the DNA-repair gene XRCC2, is associated with a lowered risk for breast cancer based on a study of 1,100 Cypriot women. The odds ratio for the His-encoding rs3218536(A) allele carriers is homozygote is 0.79, CI: 0.62-1.00, p=0.05. rs3218536(A) carriers also appear to be at lower risk for epithelial ovarian cancer. In a study of ~1,600 cases, the odds ratio for rs3218536(A;G) heterozygotes was 0.8 (CI: 0.7-1.0) and for the (quite rare) rs3218536(A;A) homozygotes 0.3 (0.1-0.9).

Parkinson's disease
31.7	rs838552 (C;T)

			linked to late onset Parkinson's disease
49.2	rs287235 (C;C) ambig

			The (G) allele of this snp has been implicated in a somewhat increased risk of developing late onset Parkinson's disease
100.0	rs283413 (G;G)	common

			SNP rs283413, also known as G78stop, encodes a rare variant of the ADH1C gene that leads to a truncated alcohol dehydrogenase protein. These types of proteins are involved in detoxification and may be linked to neurodegenerative diseases. Originally identified in three Swedish patients with Parkinson's disease (PD), a study of ~1000 PD patients vs. ~1000 controls indicated an odds ratio for the risk allele of 3.25 (CI:1.31-8.05). [This risk is effectively for heterozygotes, since the risk allele is so rare that no homozygotes for it were observed.] In a study of 40 index cases, 10% were found to harbor the rs283413(T) risk allele.

Pre-eclampsia
None	rs4762 (G;G)	(?)normal risk

			rs4762, a SNP in the angiotensin II AGT gene, has been reported to be associated with increased risk for developing pre-eclampsia, based on a study of ~180 French-Canadian women. The odds ratio associated with the rs4762(T) allele (encoding methionine) was 1.9 (CI:1.22.9, p=0.0033). Note that rs4762 is commonly referred to in the literature as 'T174M' or 'Thr174Met'; however, databases now indicate that the amino acid that varies is #207 (not 174), as the protein is currently numbered. rs4762 was also reported to play the major role in the 2.1 fold increased risk (CI: 1.4-3.4, p=0.0008) for pre-eclampsia of the rs3889728(A)-rs4762(T)-rs699(C) haplotype.
None	rs5186 (A;A)	normal risk

			rs5186 is a SNP known as +1166A/C, located in the 3' untranslated region of the angiotensin II receptor type 1 gene AGTR1, which is also known as AT2R1 or AT1R. It is among the most studied of over 50 SNPs in AGTR1. The rs5186(C) allele is associated with increased risk for essential hypertension in Caucasian populations with an odds ratio of 7.3 (homozygote (C;C) compared to (A;C) and (A;A), CI: 1.9-31.9,p=0.0015).[PMID 8021009, PMID 9084931] There are likely to be ethnic differences in risk; while the rs5186(C) allele was associated with hypertension in a Chinese population , it was not been observed as a risk in a Japanese population. Age and gender may also influence risk, as discussed in a review of AGTR1 SNPs and their role in hypertension and related disorders. Pregnant women who ar...

Premature birth
13.3	rs2298668 (A;C)

		Women with the snp has been linked to significant risk of a premature birth These [http://www.eurekalert.org/pub_releases/2006-08/vcu-gvi081606.php press] [http://www.eurekalert.org/pub_releases/2006-08/modb-rdg081706.php releases] explain it more simply The risky variation is 3x more common in women of african descent. *rs2298668 Prolylcarboxypepdiase E112D (rs2298668)D allele alone and jointly with chronic hypertension were associated with a significantly increased risk of preeclampsia
93.3	rs4986790 (A;A)

		rs4986790, a SNP also known as Asp299Gly in the TLR4 gene, is often studied along with a cosegregating SNP known as Thr399Ile, rs4986791. (TLR4 encodes a receptor involved in the innate immune response.) Together, these SNPs have been reported to be associated with a wide variety of both infectious and non-infectious diseases, although there are conflicting or even contradictory results also reported in some cases. The risk allele for rs4986790 is (G). Reported associations include : * Diabetic neuropathy ** These SNPs may be protective * Heart disease Men with the risk alleles for both SNPs are at increased risk for myocardial infarction in this study of over 2000 individuals. rs4986790(G) carriers are not at increased risk for myocardial infartions, at least in this study of ~200...
93.3	rs4986791 (C;C)

		rs4986791, a SNP also known as Thr399Ile in the TLR4 gene, is often studied along with a cosegregating SNP known as Asp299Gly, rs4986790. (TLR4 encodes a receptor involved in the innate immune response.) Together, these SNPs have been reported to be associated with a wide variety of both infectious and non-infectious diseases, although there are conflicting or even contradictory results also reported in some cases. The risk allele for rs4986791 is (T). Reported associations include : * Diabetic neuropathy ** These SNPs may be protective * Heart disease Men with the risk alleles for both SNPs are at increased risk for myocardial infarction in this study of over 2000 individuals. rs4986790(G) carriers are not at increased risk for myocardial infartions, at least in this study of ~200...

Prostate cancer
11.7	rs2987983 (A;A)	(?)normal risk

			In one large Swedish study, men with one or two rs2987983(C) alleles were reported to be at somewhat increased (odds ratio 1.22) risk for Prostate cancer compared to men homozygous for the wild type rs2987983(T) allele, however the risk can be reduced by adding phytoestrogens to the diet.
13.3	rs1447295 (A;C)	1.7x increased risk of [[prostate cancer]]

			rs1447295 is a SNP on chromosome 8q24, associated with increased risk for prostate cancer in several studies. In a study of over 3,600 Caucasians with prostate cancer, rs1447295 is one of five SNPs used (with family history as a sixth factor) to cumulatively predict overall risk. On their own, the rs1447295(A;A) and (A;C) risk genotypes yield an odds ratio for developing prostate cancer of 1.22 (CI: 1.06-1.40, p=5.3x10-3) and may account for 5.4% of population attributable risk. [http://www.pharmalive.com/News/index.cfm?articleid=428514&categoryid=40] The rs1447295 location could be responsible for about seven percent of prostate cancer cases in white men of north European descent. Thus, taken together with rs6983267, these two genetic changes could account for as much as one quarter of Pr...
18.3	rs6983267 (G;G)	1.58x risk for prostate cancer; also colon cancer

			rs6983267 is a SNP on chromosome 8q24, associated with increased risk for prostate cancer in several studies. In studies dividing the 8q24 region, this SNP falls in region 3. In a study of over 3,600 Caucasians with prostate cancer, rs6983267 is one of five SNPs used (with family history as a sixth factor) to cumulatively predict overall risk. On their own, the rs6983267(G;G) and (G;T) risk genotypes yield an odds ratio for developing prostate cancer of 1.37 (CI: 1.18-1.59, p=3.4-10e-5) and may account for 22.2% of population attributable risk. The increased risk of developing prostate cancer associated with rs6983267 now appears to be independent of the risk associated with it's close neighbor, rs1447295. The odds ratio for heterozygotes is estimated to be 1.26 (CI: 1.13 - 1.41), and for ...
21.7	rs5945572 (G;G)

			Associated with prostate cancer
31.7	rs251177 (C;T)	somewhat higher risk for prostate cancer

			rs251177 is one of seven SNPs found in a combined study of over 1,000 patients to be associated with increased risk for prostate cancer. The risk allele for this SNP is (C); and while the odds ratio was not specifically reported, the probability of false significance (not permuted though) was given as p=0.000188, using an additive model of risk.
36.7	rs7652331 (C;T)	normal risk

			rs7652331 is one of seven SNPs found in a combined study of over 1,000 patients to be associated with increased risk for prostate cancer. The risk allele for this SNP is (T); and while the odds ratio was not specifically reported, the probability of false significance (not permuted though) was given as p=4.4 x 10e-5, using a dominant model of risk.
37.3	rs1545985 (A;G)	somewhat higher risk for prostate cancer

			rs1545985 is one of seven SNPs found in a combined study of over 1,000 patients to be associated with increased risk for prostate cancer. The risk allele for this SNP is (G); and while the odds ratio was not specifically reported, the probability of false significance (not permuted though) was given as p=6.6 x 10e-6, using an additive model of risk.
41.7	rs1571801 (A;C)	1.36x risk for prostate cancer

			In a study of ~1000 Caucasian patients with prostate cancer, rs1571801 was the SNP most associated with not only prostate cancer, but having an aggressive form of it. The odds ratio for aggressive prostate cancer associated with the risk allele, rs1571801(A), was 1.36 (CI: 1.13 - 1.65, p = 0.001). The odds ratio associated with (nonaggressive) prostate cancer was also higher than average for this SNP; for the same (A) risk allele, it was 1.27 (CI: 1.10 - 1.48, p = 0.0017). Although the association was found in a study of Caucasian patients, it was also reported to be statistically significant in a population of 210 African-Americans with prostate cancer. According to [http://www.oncology-information.com/CancerLineHCP/6096_31566_2__.aspx], 'The odds ratio for aggressive prostate cancer ra...
46.7	rs10492519 (A;G)	somewhat higher risk for prostate cancer

			rs10492519 is one of seven SNPs found in a combined study of over 1,000 patients to be associated with increased risk for prostate cancer. The risk allele for this SNP is (G); and while the odds ratio was not specifically reported, the probability of false significance (not permuted though) was given as p=5.6 x 10e-6, using an additive model of risk.
48.3	rs2107301 (C;C)	normal risk

			rs2107301 is a SNP in the vitamin D VDR receptor gene. rs2107301(T;T) homozygotes were associated with an ~2.5x higher risk of prostate cancer compared to homozygote carriers of the more common (C) allele in the 630 Caucasian patients studied.
50.0	rs4880 (C;T)

			The rs4880(T) allele, part of the codon for amino acid valine at codon 16 of the antioxidant protein from the mitochrondrial superoxide dismutase 2 SOD2 gene, is the most common in most populations studied. The rs4880(C) allele gives rise to an alanine at this position. There appears to be some conflict in the literature over the effect of this SNP. Having a valine at codon 16 is said to reduce enzyme activity , and thus lead to increased oxidative stress, yet in at least one study of the actual enzyme levels measured in people, SOD2 activity was 33% higher in (C;T) or (T;T) individuals compared to (C;C) individuals . Regardless of how this resolves, several phenotypic associations have been reported for this SNP, including: * A 10 fold higher risk for heart disease in hereditary hemochrom...
53.3	rs1859962 (G;T)	normal risk
			This is the genotype of User:Watson
			rs1859962 is a SNP on chromosome 17q24.3, associated with increased risk for prostate cancer in several studies. In a study of over 3,600 Caucasians with prostate cancer, rs1859962 is one of five SNPs used (with family history as a sixth factor) to cumulatively predict overall risk. On its own, the rs1859962(G;G) risk genotype yields an odds ratio for developing prostate cancer of 1.28 (CI: 1.11-1.47, p=5.5x10e-4) and may account for 6.5% of population attributable risk. [http://www.cancerpage.com/news/article.asp?id=11059 news] linked to Prostate cancer and type-2 diabetes [http://cancergenetics.wordpress.com/2008/02/15/prostate-cancer-oldnew-snps-and-decodeprca/ cancer-genetics] these snps influence genetic risk for prostate cancer the haplotype rs6983267 rs1016343 rs4242384 rs7501939 ...
56.7	rs4430796 (A;G)	normal risk

			rs4430796 is a SNP in the TCF2 gene on chromosome 17q12, associated with increased risk for prostate cancer in several studies. In a study of over 3,600 Caucasians with prostate cancer, rs4430796 is one of five SNPs used (with family history as a sixth factor) to cumulatively predict overall risk. On its own, the rs4430796(A;A) risk genotype - in dbSNP orientation, not as published - yields an odds ratio for developing prostate cancer of 1.38 (CI: 1.21-1.57, p=1.6x10e-6) and may account for 10.2% of population attributable risk. [http://www.cancerpage.com/news/article.asp?id=11059] linked to Prostate cancer and type-2 diabetes
61.7	rs13149290 (C;C)	somewhat higher risk for prostate cancer

			rs13149290 is one of seven SNPs found in a combined study of over 1,000 patients to be associated with increased risk for prostate cancer. The risk allele for this SNP is (C); and while the odds ratio was not specifically reported, the probability of false significance (not permuted though) was given as p=2.5 x 10e-5, using a dominant model of risk.
61.7	rs629242 (C;C)	normal risk

			rs629242 is one of seven SNPs found in a combined study of over 1,000 patients to be associated with increased risk for prostate cancer. The risk allele for this SNP is (T); and while the odds ratio was not specifically reported, the probability of false significance (not permuted though) was given as p=7.2 x 10e-7, using an additive model of risk.
95.0	rs2740574 (A;A)

			rs2740574(G) alleles are associated with an ~10 fold higher risk of aggressive prostate cancer in African American males. [PMID 16414488, OMIM [http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=124010

Redheads
74.1	rs1805007 (C;C)	normal risk

			rs1805007, known as Arg151Cys or R151C, one of several SNPs in the MC1R gene associated with red hair (redheads), and in redheaded females, linked to being more responsive to the anesthetics pentazocine, nalbuphine, and butorphanol, often used by dentists [PMID 9571181, PMID 12663858, PMID 18488028] The risk allele is rs1805007(T), compared with the wild-type rs1805007(C) allele. The risk allele has also been reported in several studies to be associated with increased risk for melanoma. For example, an odds ratio of 2.94 (CI: 1.04-8.31) has been reported for an Italian population , and similarly an odds ratio of 2.9 has been reported for a Polish population . [http://yannklimentidis.blogspot.com/2008/02/mc1r-genotypes-skin-cancer-risk-and.html blog] about designing melanocortin analogs spe...
None	rs1805008 (C;C)

			rs1805008, known as Arg160Trp or R160W, is one of several SNPs in the MC1R gene associated with red hair (redheads), in this case in an Irish population although this has also been reported in Icelandic and Dutch populations . The risk allele is rs1805008(T), compared with the wild-type rs1805008(C) allele. [http://yannklimentidis.blogspot.com/2008/02/mc1r-genotypes-skin-cancer-risk-and.html blog] about designing melanocortin analogs specific to these genotypes. See also [http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=155555&a=155555_AllelicVariant0005 OMIM 155555.0005]

Restless legs syndrome
35.6	rs2300478 (G;T)	1.7x risk for restless legs

			rs2300478, a SNP located in the MEIS1 gene, has been linked to restless legs syndrome, a common sleep disorder, with an overall odds ratio of 1.78 (CI: 1.52-2.09) for the (G) risk allele. The association from this region that gives the highest association to restless legs syndrome, however, is a haplotype consisting of the rs6710341(A) and rs12469063(G) alleles. This haplotype gives rise to an odds ratio of 2.75 (CI: 2.23-3.41).
37.9	rs3923809 (A;G)	1.9x risk for restless legs

			This SNP, located in an intron of the BTBD9 gene, has a variant that is seen somewhat more frequently in individuals with restless legs syndrome. The risk allele is rs3923809(A); carriers of two such alleles, i.e. those with rs3923809(A;A) genotypes, are estimated to be 1.9 fold more likely to have restless legs syndrome than rs3923809(G;G) individuals. The authors of this study suggest that perhaps half of the cases of restless legs syndrome may involve the rs3923809 risk genotypes. Consistent with this finding, another report about rs3923809 links the (G) minor allele to a lower frequency of restless legs syndrome with an overall odds ratio of 0.57 (CI: 0.48-0.68). Note that 70-80% of all individuals in European populations carry one or two copies of the (A) major allele, yet restless ...
45.0	rs3784709 (C;C)	common

			rs3784709, a SNP located in a region of chromosome 15q, has been linked to a lower frequency of restless legs syndrome, a common sleep disorder, with an overall odds ratio of 0.71 (CI: 0.60-0.83) for the (T) minor allele.
45.8	rs12593813 (G;G)	common

			rs12593813, a SNP located in a region of chromosome 15q, has been linked to a lower frequency of restless legs syndrome, a common sleep disorder, with an overall odds ratio of 0.71 (CI: 0.60-0.83) for the (A) minor allele.
45.8	rs11635424 (G;G)	common

			rs11635424, a SNP located in a region of chromosome 15q, has been linked to a lower frequency of restless legs syndrome, a common sleep disorder, with an overall odds ratio of 0.70 (CI: 0.59-0.82) for the (A) minor allele.
60.7	rs4714156 (C;C)	common

			rs4714156, a SNP located in the BTBD9 gene region, has been linked to a lower frequency of restless legs syndrome, a common sleep disorder, with an overall odds ratio of 0.61 (CI: 0.51-0.74) for the (T) minor allele.
62.7	rs9357271 (T;T)	common

			rs9357271, a SNP located in the BTBD9 gene region, has been linked to a lower frequency of restless legs syndrome, a common sleep disorder, with an overall odds ratio of 0.63 (CI: 0.52-0.75) for the (C) minor allele.
63.3	rs9296249 (T;T)	common

			rs9296249, a SNP located in the BTBD9 gene region, has been linked to a lower frequency of restless legs syndrome, a common sleep disorder, with an overall odds ratio of 0.62 (CI: 0.52-0.75) for the (C) minor allele.

Rheumatoid Arthritis
0.0	rs2476601 (A;A)	>2x risk for T1D, RA, Addison's

			This SNP, located in the PTPN22 gene and also known as R620W, or 1858C>T, may influence Rheumatoid Arthritis and other autoimmune diseases, including but not limited to, multiple sclerosis, Crohn's disease, celiac disease and type-1 diabetes. The risk allele (in dbSNP orientation) is rs2476601(A). Note that rs6679667 and rs2476601 are reported to be perfectly correlated, so SNP determination of one predicts the other. In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for type-1 diabetes for this SNP was recalculated to be 1.98 (CI 1.822.15). rs2476601 was confirmed in another 2007 study to be a risk factor for RA . * confirms the association of rs2476601 rheumatoid arthritis * two copies of the PTPN22 R620W allele more than doubles the ris...
20.3	rs6457617 (T;T)	5.2x risk

			rs6457617 has been reported in a large study to be associated with rheumatoid arthritis. This SNP is reported to be the most statistically significant of many SNPs similarly located in the MHC region. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated with heterozygotes is 2.36 (CI 1.97-2.84), and for homozygotes, 5.21 (CI 4.31-6.30).
25.9	rs7528684 (A;A)	normal

			rs7528684 rs3792876 and rs2268277 failed to showed a statistically significant association with rheumatoid arthritis rs7528684 has been reported to be associated with rheumatoid arthritis in a Caucasian population, following reports of a similar association in a Japanese population. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 0.95 (CI 0.83-1.08), and for homozygotes, 2.30 (CI 1.64-3.23). In a study of 645 Caucasians from Southern Spain with multiple sclerosis, the rs7528684(G) allele (in dbSNP orientation) was found to be somewhat protective (per allele odds ratio 0.81, CI: 0.70-0.94, p=0.007). In another report , a summary indicates the following regarding disease and odds ratio (OR)for rs7528684: * for rheumatoid arthritis: OR =...
26.7	rs7574865 (G;T)	1.3x risk for RA; 1.5x for SLE

			rs7574865, a SNP in the third intron of the STAT4 gene, has been reported in a large study of Swedes to be associated with both rheumatoid arthritis and lupus (SLE). The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated the presence of a risk allele was 1.3 for rheumatoid arthritis and 1.55 for lupus (SLE). The paper states that, 'Homozygosity of the risk allele, as compared with absence of the allele, was associated with a more than doubled risk for lupus and a 60% increased risk for rheumatoid arthritis.' A study of 124 Caucasian patients with primary Sjogren's syndrome, a related autoimmune disease to RA and SLE, also found that the rs7574865(T) allele to be associated with higher risk for this condition (p=0.01).
26.7	rs3761847 (G;G)	>1.3x risk

			rs3761847, a SNP located between two genes associated with chronic inflammation (TRAF1 and C5), is associated with increased risk of antiCCP-positive rheumatoid arthritis. The risk allele is (G); the odds ratio reported is 1.32 (95% confidence interval, 1.23 to 1.42; P=4x1014) .
38.3	rs3738919 (C;C)	1.9x risk

			rs3738919, a SNP located in the ITGAV gene, was identified in a European study to be associated with rheumatoid arthritis (RA). The risk allele for rs3738919 is the more common allele, (C). For the three European Caucasian populations studied (372 RA patients + 330 controls), and combining the (C;C) and (A;C) genotypes in comparison to the (A;A) genotype, the odds ratio for RA = 1.94 (CI: 1.32.9, p = 0.002). There was no significant difference in RA risk between those carrying one or two (C) alleles. An editorial about this finding has been published.
50.8	rs3087243 (A;G)	increased risk for auto-immune diseases

			The rs3087243 SNP is also known in the literature as the CT60 G>A or the +6230G>A polymorphism, and it is located in the CTLA4 gene. In Asian (Japanese) populations, the presence of an rs3087243(G) allele represents a 1.3 fold increased risk of autoimmune thyroid disease, and for those with autoimmune thyroid disease, a 1.5 fold increased risk of type-1 diabetes. However, in individuals without autoimmune thyroid disease, no association was seen between this SNP and type-1 diabetes. The authors speculate that earlier studies may have reported associations between this SNP and type-1 diabetes that were actually primarily based on the association with autoimmune thyroid disease. This same SNP, rs3087243, has also been implicated as a (minor) risk factor for developing rheumatoid arthritis (...
81.7	rs2837960 (T;T)	normal

			rs2837960 has been reported in a large study to be associated with rheumatoid arthritis. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 0.95 (CI 0.83-1.08), and for homozygotes, 2.30 (CI 1.64-3.23).
89.8	rs11162922 (A;A)	2x risk

			rs11162922 has been reported in a large study to be associated with rheumatoid arthritis. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.27 (CI 0.41-4.01), and for homozygotes, 2.00 (CI 0.64-6.20).
100.0	rs2230500 (G;G)	normal risk

			A common SNP only in Asian populations, this SNP (also known as 1425G/A) and a close neighbor also in the PRKCH gene, rs3783799, have been associated with higher risk for subcortical silent brain infarction, a common form of stroke. In one study of ~1100 Japanese stroke patients, the odds ratio for carriers of the rs2230500(A) risk allele was reported as 1.40 (CI: 1.23-1.59, p=5x10e-7). A subsequent study reported the odds ratio for carriers of the (A) allele as 1.27 (CI: 1.09-1.48, p=0.0026) compared to individuals homozygous for rs2230500(G), based on studies of ~300 Japanese patients.

Schizophrenia
25.0	rs6675281 (C;T)

			linked to schizophrenia
25.0	rs4680 (A;A)	multiple associations, see details

			rs4680 is a well studied SNP in the catechol-O-methyltransferase COMT gene. rs4680 is also known as the Val158Met polymorphism; note that rs4680(G) encodes the Val, considered to be the high enzymatic activity form, and rs4680(A) encodes the Met (lower enzymatic activity). Part of a three-marker haplotype rs737865-rs4680-rs165599 rs4680, a functional Val/Met polymorphism, showed modest association with Irish familial schizophrenia. Haplotype A-G-A for SNPs rs737865-rs4680-rs165599 was preferentially transmitted to the affected subjects. A study of 400 individuals reported that an increase in plasma total homocysteine (tHcy) of 10.4% (CI: 0.01-0.21, p=0.03) for associated with rs4680(A;A) homozygotes compared with rs4680(G;G) subjects. The (A;A) genotype was also more common, but statistica...
28.3	rs6280 (C;T)	normal

			rs6280 is a SNP in the dopamine receptor D3 DRD3 gene. The rs6280(C) allele encodes a glycine, and the (T) allele encodes a serine (in dbSNP orientation). In a study of 88 patients being treated for schizophrenia with olanzapine, those who were rs6280(C;C) homozygotes had greater positive symptom remission (endpoint rating of minimal or none on all PANSS clinical response positive items, 39.1%), as compared with (C;T) or (T;T) genotypes (13.8%; p = 0.033).
30.2	rs4950928 (C;G) ambig

			rs4950928 in CHI3L1 is likely to play roles in the predisposition to schizophrenia.
35.0	rs10790212 (C;T)

			Category:is a snp associated with schizophrenia rs10790212-rs4938445-rs497768
36.7	rs2437896 (C;T)

			This SNP was identified as a 'core' SNP helping to define one (of nine total) runs of homozygosity (ROH) potentially associated with increased risk for schizophrenia. Each region consists of at least 100 consecutive SNPs, generally spanning 500KB or more, for which both chromosomes in an individual were homozygous. The overall odds ratio for schizophrenia associated with inheriting 1, 2, or 3 of these 9 ROHs was calculated to be 3.3, 5.4, or 24, respectively, with 95% confidence intervals of (1.9-5.7), (3.7-16.1), and (6.9-83.9), respectively. This particular SNP, rs2437896, was deemed to be the core SNP of a region on chromosome 2 with 115 SNPs spanning 774KB from 2:175671012 to 2:176445047 (build 35). Potentially independent of the ROH, the risk allele for this SNP in the orientation as ...
43.3	rs839523 (A;G)

			linked to schizophrenia with rs7598440, rs839523, and rs707284
45.0	rs7582658 (A;G)

			This SNP was identified as a 'core' SNP helping to define one (of nine total) runs of homozygosity (ROH) potentially associated with increased risk for schizophrenia. Each region consists of at least 100 consecutive SNPs, generally spanning 500KB or more, for which both chromosomes in an individual were homozygous. The overall odds ratio for schizophrenia associated with inheriting 1, 2, or 3 of these 9 ROHs was calculated to be 3.3, 5.4, or 24, respectively, with 95% confidence intervals of (1.9-5.7), (3.7-16.1), and (6.9-83.9), respectively. This particular SNP, rs7582658, was deemed to be the core SNP of a region on chromosome 2 with 274 SNPs spanning 2282KB from 2:188489676 to 2:190772106 (build 35). Potentially independent of the ROH, the risk allele for this SNP in the orientation as...
46.7	rs175174 (A;A)

			This snp in the gene ZDHHC8 does not appear to have any link to schizophrenia despite being quite popular in pubmed
48.3	rs707284 (A;G)

			linked to schizophrenia with rs7598440, rs839523, and rs707284
50.0	rs3738401 (G;G)

			rs3738401 is a SNP in the DISC1 gene, known as R264Q. Associated with schizophrenia 13 single-nucleotide polymorphisms (SNPs) in 723 members of 179 Finnish Bipolar disorder families. rs751229(T) and rs3738401(A) was over-transmitted to males with psychotic disorder. under-transmitted rs821616(T) and rs1411771(T) *The risk haplotype for psychotic disorder also associated to perseverations (P = 0.035; for rs751229 alone P = 0.0012), and a protective haplotype G-T-G with rs1655285 in addition to auditory attention (P = 0.0059).
55.0	rs17651507 (A;A) ambig

			This SNP was identified as a 'core' SNP helping to define one (of nine total) runs of homozygosity (ROH) potentially associated with increased risk for schizophrenia. Each region consists of at least 100 consecutive SNPs, generally spanning 500KB or more, for which both chromosomes in an individual were homozygous. The overall odds ratio for schizophrenia associated with inheriting 1, 2, or 3 of these 9 ROHs was calculated to be 3.3, 5.4, or 24, respectively, with 95% confidence intervals of (1.9-5.7), (3.7-16.1), and (6.9-83.9), respectively. This particular SNP, rs17651507, was deemed to be the core SNP of a region on chromosome 17 with 211 SNPs spanning 1453KB from 17:141169023 to 17:42622984 (build 35). Potentially independent of the ROH, the risk allele for this SNP in the orientation...
56.7	rs7598440 (C;T)

			linked to schizophrenia with rs7598440, rs839523, and rs707284
100.0	rs947267 (A;C)

			showed that rs947267 was significantly associated with schizophrenia rs778294 and rs947267 associated with the risk of schizophrenia, however rs947267, showed an opposite direction of genetic effect on schizophrenia risk here than in a previous study
None	rs1801028 (G;G) ambig	normal risk

			rs1801028 is a SNP in the dopamine D2 receptor DRD2 gene. A meta-analysis comprising 27 samples and over 3,707 schizophrenia patients concluded that Cys/Ser heterozygotes, i.e. rs1801028(C;G) genotypes, were at elevated risk for schizophrenia when compared to either homozygote genotype (rs1801028(C;C) or rs1801028(G;G)). The odds ratio was 1.4 (p<0.005). An earlier meta-analysis comprising over 9,000 schizophrenia patients concluded pretty much the same thing: the Cys311 (rs1801028(G)) allele frequency led to an odds ratio of 1.43 (CI: 1.16-1.78, p<0.001) for this risk allele. A study of ~120 Chinese patients with schizophrenia concluded that Cys/Ser heterozygotes may not respond to [risperidone treatment as well as Ser/Ser homozygotes. A paper has been published describing mistakes made i...
None	rs165599 (A;A)

			anxiety-related personality traits, ADHD, schizophrenia part of a three marker haplotype rs737865-rs4680-rs165599 epistasis between SNPs in COMT (rs2097603, Val158Met (rs4680), rs165599) and polymorphisms in other schizophrenia susceptibility genes popular in pubmed is associated with bipolar disorder and influences prefrontal aspects of verbal memory in bipolar patients and healthy controls.
None	rs6277 (G;G)	(?)1.6x higher schizophrenia risk

			rs6277 is one of several SNPs in the dopamine receptor DRD2 gene. In a study of 300+ Russian patients with schizophrenia, the rs6277(C) allele was associated with higher risk. From a pooled meta-study (total of 4 other reports plus this one) the allelic odds ratio is 1.42 (CI: 1.26-1.61, p<0.00005), and the genotypic odds ratio for the (C;C) genotype was 1.6 (CI: 1.32-1.95, p<0.00005). Note that rs6275 and rs6277 are only 18bp apart, hence their very tight linkage (r²=1).

Sciatica
23.3	rs1800795 (G;G) ambig	more IL6; certain risks, see details
			rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. In the literature, it is almost universally referred to as the IL6 '-174' polymorphism. It tends to be quite polymorphic in Caucasians, but Asian and African populations are almost monomorphic (for the (G) allele). The rs1800795(G) allele, generally associated with higher levels of IL6, has been associated with increased risk in the following studies: * The rs1800795(G) allele was significantly associated with type-2 diabetes (odds ratio 1.51, CI: 1.11-2.07, p=0.0096) in a study of 700 elderly Caucasians. * Following a kidney transplant, patients with rs1800795(G;G) genotypes have a higher risk of new-onset diabetes an...
			rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. In the literature, it is almost universally referred to as the IL6 '-174' polymorphism. It tends to be quite polymorphic in Caucasians, but Asian and African populations are almost monomorphic (for the (G) allele). It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. Studies on rs1800795 now include potential associations with heart disease, Kaposi's sarcoma, type-2 diabetes, stroke, obesity, Hodgkin's lymphoma, sudden ...
28.3	rs1800797 (G;G)

			rs1800797, rs1800796 and rs1800795 have been shown to affect both the transcription and secretion of IL-6, to symptomatic distal interphalangeal osteoarthritis based on 535 women. the G alleles of two promoter single-nucleotide polymorphisms (SNP) G-597A and G-174C were more common among the subjects with symptomatic DIP OA than among those with no disease (p-values corrected for multiple testing 0.020 and 0.024). Also, the carriage of at least one G allele in these positions increased the risk of disease (p=0.006 and, p=0.008, respectively). Carrying a haplotype with the G allele in all three promoter SNPs increased the risk of symptomatic DIP OA more than four-fold (OR 4.45, p=0.001). Carriage of the G-G diplotype indicated an increased risk of both symmetrical DIP OA (OR 1.52 95% CI 1.0...
91.4	rs1800796 (G;G) ambig

			rs1800796 IL-6 572G>C polymorphism (and h.211 haplotype) is associated with Abdominal Aortic Aneurysm (AAA) [PMID 17508011 Our results provide evidence that there is a clear genetic influence of IL6 -572C>G polymorphism on plasma levels of fibrinogen and CRP, but this polymorphism does not lead to elevated blood pressure. rs1800797, rs1800796 and rs1800795 have been shown to affect both the transcription and secretion of IL-6, to symptomatic distal interphalangeal osteoarthritis based on 535 women. the G alleles of two promoter single-nucleotide polymorphisms (SNP) G-597A and G-174C were more common among the subjects with symptomatic DIP OA than among those with no disease (p-values corrected for multiple testing 0.020 and 0.024). Also, the carriage of at least one G allele in these posi...

Secondhand smoke susceptibility
35.0	rs1695 (A;A)	normal

			This snp, in the GSTP1 gene influences asthma risk mentioned in this [http://news.bbc.co.uk/2/hi/uk_news/scotland/tayside_and_central/5251968.stm bbc article] also known as GSTP1Val105, or GSTP1 Ile105Val This [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16882827&query_hl=1&itool=pubmed_docsum research paper] shows that 13- to 21-year-olds exposed to tobacco smoke at home, with this mutation had more severe asthma than those without the mutation. Several papers published findings associating GSTP1 Ile105Val genotypes with bronchial, childhood, or atopic asthma. Note that some studies, however, have not observed any association between this SNP and asthma in certain populations , or even more paradoxically, have observed that rs1695(G;G)...

Skin cancer
74.1	rs1805007 (C;C)	normal risk

			rs1805007, known as Arg151Cys or R151C, one of several SNPs in the MC1R gene associated with red hair (redheads), and in redheaded females, linked to being more responsive to the anesthetics pentazocine, nalbuphine, and butorphanol, often used by dentists [PMID 9571181, PMID 12663858, PMID 18488028] The risk allele is rs1805007(T), compared with the wild-type rs1805007(C) allele. The risk allele has also been reported in several studies to be associated with increased risk for melanoma. For example, an odds ratio of 2.94 (CI: 1.04-8.31) has been reported for an Italian population , and similarly an odds ratio of 2.9 has been reported for a Polish population . [http://yannklimentidis.blogspot.com/2008/02/mc1r-genotypes-skin-cancer-risk-and.html blog] about designing melanocortin analogs spe...
None	rs1015362 (T;T)	(?)normal

			rs1015362 is a SNP near the ASIP (agouti signaling protein) gene on chromosome 20. This SNP is one of a tightly-linked pair that increases the likelihood of an individual being prone to sun sensitivity, in other words, freckles and sunburn, based on a study of 6,000+ Caucasians (5,000+ Icelanders + 1,000+ Dutch). The odds ratios, presumably on a dominant basis, and at least in the largest population (Icelanders) for 'freckles and burns vs. no freckles and tans' for the haplotype pair rs1015362(G) - rs4911414(T) is 3.91 (CI: 2.54-6.03) for males and 2.42 (CI: 1.52-3.86) for females, with an overall p=0.051. Based on a study by the same authors of 4,000+ skin cancer patients, this haplotype was seen to confer significant increased risk for cutaneous malignant melanoma (odds ratio 1.45, p = 1...
None	rs1805008 (C;C)

			rs1805008, known as Arg160Trp or R160W, is one of several SNPs in the MC1R gene associated with red hair (redheads), in this case in an Irish population although this has also been reported in Icelandic and Dutch populations . The risk allele is rs1805008(T), compared with the wild-type rs1805008(C) allele. [http://yannklimentidis.blogspot.com/2008/02/mc1r-genotypes-skin-cancer-risk-and.html blog] about designing melanocortin analogs specific to these genotypes. See also [http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=155555&a=155555_AllelicVariant0005 OMIM 155555.0005]
None	rs4911414 (T;T)	2-4x higher risk of sun sensitivity if part of risk haplotype

			rs4911414 is a SNP near the ASIP (agouti signaling protein) gene on chromosome 20. This SNP is one of a tightly-linked pair that increases the likelihood of an individual being prone to sun sensitivity, in other words, freckles and sunburn, based on a study of 6,000+ Caucasians (5,000+ Icelanders + 1,000+ Dutch). The odds ratios, presumably on a dominant basis, and at least in the largest population (Icelanders) for 'freckles and burns vs. no freckles and tans' for the haplotype pair rs1015362(G) - rs4911414(T) is 3.91 (CI: 2.54-6.03) for males and 2.42 (CI: 1.52-3.86) for females, with an overall p=0.051. Based on a study by the same authors of 4,000+ skin cancer patients, this haplotype was seen to confer significant increased risk for cutaneous malignant melanoma (odds ratio 1.45, p = 1...

Skin color
95.0	rs1426654 (A;A)	probably light-skinned, European ancestry

			This SNP influences skin pigmentation. The allele p.A111T, rs1426654(A), indicates light-skinned european ancestry. [PMID 16847698, PMID 16357253] It appears as if this SNP is a relatively new one in human evolution; one estimate is that the rs1426654(A) allele, in other words, light skin pigmentation, spread through the European population around 6,000 - 12,000 years ago. Prior to that, 'European ancestors' were most likely relatively brown-skinned.
96.7	rs16891982 (G;G) ambig	european

			This snp influences skin pigmentation. The allele p.L374F indicates light-skinned european ancestry

Stroke
26.7	rs5443 (C;C)	average

			rs5443, a SNP in the G-protein beta3 subunit (GNB3) gene that is more commonly known as the C825T variant, has been linked to a number of metabolic conditions including obesity, coronary artery disease, insulin resistance and therefore diabetes, left ventricular hypertrophy, and hypertension. It has also been linked to how well a patient responds to Viagra (sildenafil). Several studies have been unable to replicate one or more of the associations in at least some populations between this SNP and these conditions. The more notable studies include: rs5443(T) allele carriers are 2-3 fold more likely to be obese in Caucasian, Chinese, and African American populations. rs5443(T) carriers are clearly at higher risk for hypertension, but this review indicates that whether they are also at incr...
45.0	rs173686 (C;T)

			The presence of an rs173686(C) allele has been linked to increased risk of a certain type of stroke, Intracranial Aneurysm, in a population of Dutch adults. Note: the dbSNP sequence entry for this SNP represents the noncoding strand, and is thus the reverse complement compared to the SNP as referred to in .
98.3	rs6025 (G;G)	normal/common

			rs6025 represents a SNP in the Factor V F5 gene, encoding a change in the protein from an arginine at position 506 to a glutamine. The resulting rs6025(A) allele encodes a mutation known as the Leiden mutation, R506Q, found in perhaps 3 to 5% of the individuals in most populations. About 1 in 10 individuals harboring the R506Q will experience clinically significant venous thromboembolism in their lifetimes (according to [http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=227400 OMIM]). Overall, the rs6025(A) allele appears to be necessary but not sufficient for the development of venous thromboembolism. Patients who are rs6025(A;G) heterozygotes but lack other risk-enhancing SNPs have a risk of recurrent deep venous thrombosis equal to patients with no such SNPs. In contrast, patients who ...
100.0	rs2230500 (G;G)	normal risk

			A common SNP only in Asian populations, this SNP (also known as 1425G/A) and a close neighbor also in the PRKCH gene, rs3783799, have been associated with higher risk for subcortical silent brain infarction, a common form of stroke. In one study of ~1100 Japanese stroke patients, the odds ratio for carriers of the rs2230500(A) risk allele was reported as 1.40 (CI: 1.23-1.59, p=5x10e-7). A subsequent study reported the odds ratio for carriers of the (A) allele as 1.27 (CI: 1.09-1.48, p=0.0026) compared to individuals homozygous for rs2230500(G), based on studies of ~300 Japanese patients.

Taste
48.3	rs713598 (C;G) ambig	can taste bitter
			This is the genotype of User:Watson
			rs713598 is one of three SNPs that form the main haplotypes behind the ability to perceive as bitter the taste of the compound phenylthiocarbamide (PTC) and similar molecules in foods (like cabbage and raw broccoli) or drinks (like coffee and dark beers). The rs713598(G) allele, in the orientation shown in dbSNP, is the 'tasting' allele, and it is dominant to the 'non-tasting' allele rs713598(C), so having one copy is enough to have the bitter tasting ability. If you are a 'taster', you're also likely to carry at least one rs10246939(C) and one rs1726866(C) allele since, along with rs713598(G), these three SNPs form the most common tasting haplotype. If you lack these alleles, you're quite likely (~80%) to be a non-taster of bitterness, meaning that foods that may taste bitter to others ta...
49.2	rs10246939 (C;T)	can taste bitter

			rs10246939 is one of three SNPs that form the main haplotypes behind the ability to perceive as bitter the taste of the compound phenylthiocarbamide (PTC) and similar molecules in foods (like cabbage and raw broccoli) or drinks (like coffee and dark beers). The rs10246939(C) allele, in the orientation shown in dbSNP, is the 'tasting' allele, and it is dominant to the 'non-tasting' allele rs10246939(T), so having one copy is enough to have the bitter tasting ability. If you are a 'taster', you're also likely to carry at least one rs713598(G) and one rs1726866(C) allele since, along with rs10246939(C), these three SNPs form the most common tasting haplotype. If you lack these alleles, you're quite likely (~80%) to be a non-taster of bitterness, meaning that foods that may taste bitter to oth...
50.0	rs1726866 (C;T)	can taste bitter

			rs1726866 is one of three SNPs that form the main haplotypes behind the ability to perceive as bitter the taste of the compound phenylthiocarbamide (PTC) and similar molecules in foods (like cabbage and raw broccoli) or drinks (like coffee and dark beers). The rs1726866(C) allele is the 'tasting' allele, and it is dominant to the 'non-tasting' allele rs1726866(T), so having one copy is enough to have the bitter tasting ability. If you are a 'taster', you're also likely to carry at least one rs713598(G) and one rs10246939(C) allele since, along with rs1726866(C), these three SNPs form the most common tasting haplotype. If you lack these alleles, you're quite likely (~80%) to be a non-taster of bitterness, meaning that foods that may taste bitter to others taste far less bitter to you.

Testicular cancer
47.5	rs1050565 (A;G)	normal

			Testicular cancer patients may be treated with bleomycin, a cytotoxic drug that is essential component of chemotherapy regimens for this cancer, officially known as disseminated testicular germ-cell cancer (TC). rs1050565 is a SNP in the BLMH gene. This gene encodes a protein that can inactivate bleomycin. Based on a study of 300 TC patients treated with bleomycin, a testicular cancer patient with a rs1050565(G;G) genotype has an odds ratio of 4.97 (CI: 2.17 - 11.39) for TC-related death compared to (A;G) or (A;A) genotypes. The rs1050565(G;G) genotype also shows a higher prevalence of early relapses.

Type-1 diabetes
11.7	rs2296336 (C;C) ambig	normal

			rs2296336 has been reported in a Swedish study to be associated with type-1 diabetes. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.3 (CI 1.00-1.69), and for homozygotes, 2.9 (CI 1.88-4.59). suggests this snp does not play a role in type-1 diabetes.
20.0	rs1990760 (C;T)

			[http://jcem.endojournals.org/cgi/content/abstract/92/8/3338 Abstract] associated with type-1 diabetes, organ-specific autoimmune diseases, including Graves' disease. (odds ratio 1.47 (CI: 1.231.76, p = 1.9 x 10⁵) This polymorphism may also contribute to several other autoimmune disorders. A study of 261 Chinese patients with Graves' disease failed to find any association with rs1990760.
28.8	rs11052552 (G;G)	1.4x risk

			rs11052552 has been reported in a large study to be associated with type-1 diabetes. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.49 (CI 1.28-1.73), and for homozygotes, 1.43 (CI 1.21-1.69).
45.8	rs237025 (C;T)	MET/VAL moderate [[diabetes]] susceptibility
			This [http://www.emaxhealth.com/23/6527.html press release] provides a helpful summary of . The paper concludes that in rs237025, the MET form increases the odds of type-1 diabetes. This form produces both MET and VAL. suggests the contribution of rs237025 to both type-1 diabetes\|type 1 and type-2 diabetes\|type 2 diabetes susceptibility.
			suggests the contribution of rs237025 to both type-1 diabetes\|type 1 and type-2 diabetes\|type 2 diabetes susceptibility. It is also known as Met55Val or A163G. This [http://www.emaxhealth.com/23/6527.html press release] provides a helpful summary of . The paper concludes that in the M55V mutation, the MET form increases the odds of type-1 diabetes. This was the first snpedia snp and has one of the largest (aka most difficult) Watson aligments.
49.2	rs17696736 (A;G)	1.3x risk

			rs17696736 has been reported in a large study to be associated with type-1 diabetes. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.34 (CI 1.16-1.53), and for homozygotes, 1.94 (CI 1.65-2.29). In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for this SNP was recalculated to be 1.22 (CI 1.151.28).
50.8	rs3087243 (A;G)	increased risk for auto-immune diseases

			The rs3087243 SNP is also known in the literature as the CT60 G>A or the +6230G>A polymorphism, and it is located in the CTLA4 gene. In Asian (Japanese) populations, the presence of an rs3087243(G) allele represents a 1.3 fold increased risk of autoimmune thyroid disease, and for those with autoimmune thyroid disease, a 1.5 fold increased risk of type-1 diabetes. However, in individuals without autoimmune thyroid disease, no association was seen between this SNP and type-1 diabetes. The authors speculate that earlier studies may have reported associations between this SNP and type-1 diabetes that were actually primarily based on the association with autoimmune thyroid disease. This same SNP, rs3087243, has also been implicated as a (minor) risk factor for developing rheumatoid arthritis (...
96.7	rs3772534 (G;G)

			One report based on a study of 480 Danish families indicated that the rs3772534 SNP in the CBLB gene indicated an increased risk for developing type 1 diabetes, and that there might be co-inheritance with the rs3087243 SNP found in the CTLA4 gene. However, a subsequent study based on over 2,000 parent-child trios (ie families) failed to find any evidence of either effect.

Type-2 diabetes
8.3	rs7756992 (G;G)

			rs7756992 significantly p = 0.0363 associated with type-2 diabetes in 1,630 Japanese subjects and in 1,064 controls 1,638 type 2 diabetes patients and 1,858 controls rs7756992 non-significant T2D and normal glucose tolerant (NGT) individuals. (3,295 T2D and 3,595 NGT), strong associations with T2D were found for CDKAL1 (OR(rs7756992) = 1.30[1.19-1.42], P = 2.3x10(-9)) CDKN2A/2B (OR(rs10811661) = 0.74[0.66-0.82], P = 3.5x10(-8)) IGFBP2 (OR(rs1470579) = 1.17[1.07-1.27], P = 0.0003) SNPs. T2D risk increased strongly when risk alleles, including the previously discovered T2D-associated TCF7L2 rs7903146 SNP, were combined (8.68-fold for the 14% of French individuals carrying 18 to 30 risk alleles with an allelic OR of 1.24)
8.3	rs11868035 (A;A)	1.19x increased risk for T2D

			rs11868035 is one of several SNPs associated with the SREBF1 gene that show a modest association with type-2 diabetes. A study of ~2,000 Caucasian patients (and 10,000+ controls) led to an odds ratio of 1.19 (CI: 1.07-1.33, p=0.002) for the minor (risk) allele, rs11868035(A), in the orientation as in dbSNP.
8.3	rs4712523 (G;G)

			associated with type-2 diabetes
11.7	rs8050136 (A;A)