Table 1.
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.
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.”
Odds ratio equivalent was calculated from the standardized mean difference.
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.
MAFs reported in the original GWAS were based on the International HapMap Project frequencies.