Table 1.
Loci achieving P values < 5.0 × 10−8 in the meta-analyses of Stage 1 and 2 data
| Association statistics | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Stage 1 | Stage 2 | Meta-analysisa | |||||||
| dbSNP ID | Chr: locationb Closet genes Position within gene |
Alleles Ref/Alt |
Population | OR | P | OR | P | OR (95% CI) | P value |
| rs2720378 | 4: 185568113 | C/G | Japan | 0.64 | 2.5 × 10−8 | 0.85 | 1.7 × 10−3 | 0.83 (0.78–0.89) | 1.6 × 10−8 |
| CASP3 | Korea | 0.83 | 0.15 | 1.00 | 0.96 | ||||
| intron | Taiwan | 0.81 | 6.6 × 10−3 | 1.03 | 0.78 | ||||
| rs1873212 | 6: 27869631 | C/T | Japan | 1.35 | 1.7 × 10−4 | 1.20 | 1.8 × 10−3 | 1.27 (1.18–1.36) | 2.0 × 10−10 |
| TRX-CAT1-7 | Korea | 1.43 | 0.017 | 1.34 | 0.013 | ||||
| 3′ flanking | Taiwan | 1.29 | 0.012 | 1.17 | 0.27 | ||||
| rs1778477 | 6: 28248594 | A/T | Japan | 0.79 | 0.28 | 0.76 | 7.1 × 10−5 | 0.77 (0.70–0.83) | 7.2 × 10−10 |
| PGBD1 | Korea | 0.66 | 7.2 × 10−3 | 0.83 | 0.094 | ||||
| 5′ flanking | Taiwan | 0.72 | 2.9 × 10−3 | 0.84 | 0.31 | ||||
| rs1264516 | 6: 30411903 | C/A | Japan | 1.31 | 5.2 × 10−4 | 1.21 | 2.8 × 10−4 | 1.24 (1.16–1.32) | 3.9 × 10−11 |
| LOC105375012 | Korea | 1.38 | 8.0 × 10−3 | 1.29 | 3.5 × 10−3 | ||||
| 3′ flanking | Taiwan | 1.20 | 0.27 | 1.11 | 0.35 | ||||
| rs2857602 | 6: 31533378 | G/A | Japan | 0.73 | 8.9 × 10−6 | 0.77 | 2.5 × 10−7 | 0.78 (0.73–0.83) | 2.8 × 10−15 |
| LTA | Korea | 0.67 | 1.2 × 10−3 | 0.81 | 0.027 | ||||
| intron | Taiwan | 0.86 | 0.059 | 0.84 | 0.13 | ||||
| rs3129960 | 6: 32300809 | A/G | Japan | 0.72 | 3.5 × 10−4 | 0.66 | 7.1 × 10−8 | 0.73 (0.67–0.80) | 6.7 × 10−13 |
| C6orf10/ LOC101929163 | Korea | 0.84 | 0.37 | 0.83 | 0.22 | ||||
| intron/intron | Taiwan | 0.75 | 1.7 × 10−3 | 0.83 | 0.17 | ||||
| rs7775228 | 6: 32658079 | T/C | Japan | 1.29 | 5.4 × 10−4 | 1.36 | 3.1 × 10−9 | 1.26 (1.19–1.35) | 7.0 × 10−13 |
| HLA-DQB1 | Korea | 1.07 | 0.60 | 1.05 | 0.65 | ||||
| 5′ flanking | Taiwan | 1.35 | 2.0 × 10−4 | 1.08 | 0.54 | ||||
| rs2071473 | 6: 32782605 | C/T | Japan | 1.39 | 8.4 × 10−6 | 1.29 | 1.2 × 10−6 | 1.26 (1.18–1.34) | 6.7 × 10−13 |
| HLA-DOB | Korea | 1.32 | 0.23 | 1.30 | 6.1 × 10−3 | ||||
| intron | Taiwan | 1.09 | 0.26 | 1.15 | 0.22 | ||||
| rs2736340 | 8: 11343973 | C/T | Japan | 1.71 | 1.3 × 10−9 | 1.51 | 6.2 × 10−13 | 1.55 (1.44–1.66) | 6.6 × 10−33 |
| BLK | Korea | 1.48 | 6.1 × 10−3 | 1.48 | 3.8 × 10−4 | ||||
| 5′ flanking | Taiwan | 1.56 | 2.0 × 10−7 | 1.55 | 7.6 × 10−4 | ||||
| rs4774175 | 14: 107152027 | G/A | Japan | 1.22 | 4.9 × 10−3 | 1.22 | 1.7 × 10−4 | 1.20 (1.13–1.28) | 6.0 × 10−9 |
| IGHV1-69 | Korea | 1.40 | 7.6 × 10−3 | 1.20 | 0.059 | ||||
| 3′ flanking | Taiwan | 1.16 | 0.042 | 1.06 | 0.63 | ||||
| rs28493229 | 19: 41224204 | G/C | Japan | 1.50 | 3.4 × 10−6 | 1.38 | 1.3 × 10−6 | 1.41 (1.29–1.53) | 1.1 × 10−14 |
| ITPKC | Korea | 0.98 | 0.91 | 1.25 | 0.14 | ||||
| intron | Taiwan | 1.97 | 1.9 × 10−6 | 1.24 | 0.27 | ||||
| rs1883832 | 20: 44746982 | T/C | Japan | 1.34 | 1.4 × 10−4 | 1.18 | 2.1 × 10−3 | 1.28 (1.20–1.36) | 1.5 × 10−13 |
| CD40 | Korea | 1.07 | 0.61 | 1.32 | 5.1 × 10−3 | ||||
| 5′ UTR | Taiwan | 1.41 | 4.9 × 10−6 | 1.42 | 2.3 × 10−3 | ||||
For all single nucleotide variants (SNVs), association in the logistic redression model was evaluated and odds ratios were calculated for the effects of the alternative alleles
Chr chromosomes, Ref reference allele, Alt alternative allele, OR odds ratio, CI confidence interval, UTR untranslated region
aCombined odds ratios and P values were calculated using fixed-effects meta-analytic model
bLocation of the SNVs are derived from NCBI human genome reference sequence Build 37.3