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. 2010 Sep 28;172(8):869–889. doi: 10.1093/aje/kwq234

Table 1.

Eligible Associations With a Minor Allele Frequency of 5% or Less and P ≤ 10-7

Disease/Trait Region Reported Gene(s) Variant-Risk Allele Position/Function Risk Allele Frequency Population Descent P Value Odds Ratio 95% Confidence Interval Reference
ALL 12q24.22 KRTHB5 rs2089222-A Intronic 0.03 European 8.0 × 10-8 2.26 1.60, 3.00 39
AIDS progression 6p21.33 HCP5, MICB, MCCD1, BAT1, LTB, TNF rs2395029-G Nonsynonymous coding (missense) 0.03 European 3.0 × 10-19 3.47 2.39, 5.04 40
6p21.3 C6orf48 rs9368699-C 5′-UTR 0.03 European 2.0 × 10-11 NR NR
Blue vs. green eyes 15q13.1 OCA2 rs1667394-A Intronic 0.97 European 2.0 × 10-53 3.67 2.67, 5.05 41
Freckles 16q24.3 MC1R rs1805007-T Nonsynonymous coding (missense) 0.05 European 1.0 × 10-96 3.33 2.92, 3.80
BMD (lumbar spine) 13q14 AKAP11 rs180851-C (I) Intergenica 0.95 European 2.0 × 10-12 1.46b 1.31, 1.63 42
13q14 AKAP11 rs7326472-A Intergenica 0.95 European 1.0 × 10-10 1.39b 1.24, 1.54
13q14 AKAP11 rs12854504-T (I) Intergenica 0.95 European 1.0 × 10-10 1.39b 1.24, 1.54
13q14 AKAP11 rs7998154-T (I) Intergenica 0.02 European 2.0 × 10-8 1.75b 1.46, 2.10
13q14 TNFSF11 rs6561055-G (I) Intergenica 0.95 European 3.0 × 10-10 1.39b 1.24, 1.54
13q14 TNFSF11 rs17639156-T (I) Intergenica 0.95 European 5.0 × 10-10 1.39b 1.24, 1.54
Cognitive performance Xp22.2 HCCS rs5934953-C Intronic 0.02 European 1.0 × 10-7 NR NR 43
Crohn's disease 16q12.1 NOD2 rs2066844-T Nonsynonymous coding (missense) 0.05 European 1.0 × 10-18 2.48 1.98, 3.10 37
16q12.1 NOD2 rs2066845-C Nonsynonymous coding (missense) 0.01 European 8.0 × 10-10 3.04 2.09, 4.42
16q12.1 NOD2 rs2066847-C Frameshift coding 0.04 European 3.0 × 10-49 4.30 3.42, 5.42
12q12 LRRK2, MUC19 rs11175593-T (I) Intronic 0.02 European 3.0 × 10-10 1.54 1.34, 1.76 38
HDL cholesterol 20q13.12 HNF4A rs1800961-C (I) Nonsynonymous coding (missense) 0.97 European 8.0 × 10-10 1.41b 1.27, 1.57 44
9q31.1 ABCA1 rs9282541-T Nonsynonymous coding (missense) 0.03 European, Mexicans, Asian Indians 5.0 × 10-8 1.33b c 1.21, 1.45 45
Hematocrit 6p22.1 HFE rs1800562-A (I) Nonsynonymous coding (missense) 0.04d European 2.0 × 10-9 1.74 1.45, 2.09 36
Hemoglobin 6p22.1 HFE rs1800562-A (I) Nonsynonymous coding (missense) 0.04d European 6.0 × 10-19 1.33 1.25, 1.42
LDL cholesterol 1p32.3 PCSK9 rs11591147-G Nonsynonymous coding (missense) 0.99 European 2.0 × 10-44 2.34b 2.07, 2.64 46
MCH 6p22.2 SLC17A3 rs1408272-G (I) Unknown 0.03d European 4.0 × 10-39 1.03 1.02, 1.04 36
MCV 6p22.1 HFE rs1800562-A (I) Nonsynonymous coding (missense) 0.04d European 1.0 × 10-23 12.83 7.73, 20.92 35
NCP 3p22.2 ITGA9 rs189897-A Intronic 0.03 Asian 7.0 × 10-8 3.18 1.94, 5.21 48
3p22.2 ITGA9 rs197757-T Intronic 0.03 Asian 1.0 × 10-7 3.09 1.89, 5.05
NSCL 18q22.3 Intergenic rs17085106-T Intergenic 0.02 European 4.0 × 10-8 4.07 2.37, 7.00 47
Panic disorder 12p13.31 TMEM16B rs12579350-A Intronic 0.01 Asian 4.0 × 10-9 22.11 5.30, 92.14 49
1q32.1 PKP1 rs860554-T Intronic 0.05 Asian 5.0 × 10-8 4.03 2.40, 6.76
Prostate cancer 8q24.21 Intergenic rs16901979-A Intergenic 0.03 European 1.1 × 10-12 1.79 1.53, 2.11 33
Primary biliary cirrhosis 6p21.3 C6orf10 rs2395148-A Intronic 0.02 European 4.0 × 10-14 2.87 2.16, 3.82 50
ALP 12q12 PDZRN4, CNTN1 rs1880887-C Intronic 0.03 European 1.0 × 10-10 NR NR 51
fT3 17p12 HS3ST3B1 rs3848445-C Unknown 0.05 European 8.4 × 10-9 NR NR
Psoriasis 6p21.33 HLA-C rs2395029-C Nonsynonymous coding (missense) 0.03 European 2.1 × 10-26 4.10 3.10, 5.30 52
Response to treatment for ALL 10p12.33 ST8SIA6 rs359312-T Intronic 0.04 European, African, other 9.0 × 10-8 3.91 1.52, 10.10 53
Response to antipsychotic therapy 2p12 Intergenic rs17022444-G Intergenic 0.03 European, African, other 1.0 × 10-10 NR NR 54
4q24 Intergenic rs7669317-C Intergenic 0.04 European, African, other 8.0 × 10-8 NR NR
SLE 6q23.3 TNFAIP3 rs5029939-G Intronic 0.03 European 3.0 × 10-12 2.28 1.80, 2.88 55
6q23.3 TNFAIP3 rs2230926-C Nonsynonymous coding (missense) 0.04 Asian 1.0 × 10-17 1.72 1.52, 1.94 56
Tanning 5p13.3 MATP rs35391-C Intronic 0.97 European 3.0 × 10-10 2.22 1.72, 2.86 57
Triglycerides 11q23.3 APOA1, APOC3, APOA4, APOA5 rs662799-G (I) Upstream 0.05 European 2.0 × 10-15 1.31b,c 1.22, 1.40 58
11q23.3 APOA1, APOC3, APOA4, APOA5, DSCAML1 rs10892151-A Intronic 0.03 European 3.0 × 10-29 NR NR 59
Type 1 diabetes 7p12.1 COBL rs4948088-C (I) Unknown 0.95 European 4.0 × 10-8 1.30 1.11, 1.49 60
Type 2 diabetes 10q25.2 TCF7L2 rs7903146-T Intronic 0.04 Asian 8.0 × 10-12 1.54 1.36, 1.74 61

Abbreviations: AIDS, acquired immunodeficiency syndrome; ALL, acute lymphoblastic leukemia; ALP, alkaline phosphatase; BMD, bone mineral density; fT3, free triiodothyronine; GWAS, genome-wide association study(ies); HDL, high density lipoprotein; I, risk variants imputed rather than directly genotyped; LDL, low density lipoprotein; MAF, minor allele frequency; MCH, mean corpuscular hemoglobin; MCV, mean corpuscular volume; NCP, nasopharyngeal carcinoma; NHANES, National Health and Nutrition Examination Survey; NR, not reported and data not adequate for computing the missing values; NSCL, nonsyndromic cleft lip with or without cleft palate; SLE, systemic lupus erythematosus; SNP, single-nucleotide polymorphism; 5′-UTR, 5′-untranslated region.

a

For these SNPs, AKAP11 and TNFSF11 were reported as the closest genes in the GWAS, but WGA Viewer and the Ensembl characterized them as “intergenic.”

b

Odds ratio equivalent was calculated from the standardized mean difference.

c

Odds ratio equivalent was computed from the mean difference using also the population standard deviation from NHANES data on HDL cholesterol and triglyceride levels, because the population standard deviation was not given in the GWAS.

d

MAFs reported in the original GWAS were based on the International HapMap Project frequencies.