Table 2.
Combined results for known and novel independent GWAS signals.
| Discovery Meta-analysis N=6,699 (2,747 cases & 3,952 controls) |
Replication Meta-analysis N=13,913 (4,911 cases & 9,002 controls) |
All Cohorts Combined N=20,612 (7,658 cases & 12,954 controls) |
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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| Chr | Location* (bp) | SNP ** | Risk Allele | Freq. European Controls | Freq. Asian Controls | OR | P-value | OR | P-value | OR | P-value | Q-test | I2 | Locus Name | Novel |
| 1 | 107,990,381 | rs17019602 | G | 0.19 | 0.19 | 1.20 | 4.7E-05 | 1.16 | 2.9E-05 | 1.17 | 6.8E-09 | 0.50 | 0 | VAV3 | Novel |
| 1 | 194,953,541 | rs6677604 | G | 0.80 | 0.93 | 1.36 | 3.5E-08 | 1.33 | 2.6E-07 | 1.35 | 4.8E-14 | 0.53 | 0 | CFHR3,1-del | Known |
| 6 | 32,532,860 | rs7763262 | C | 0.69 | 0.72 | 1.51 | 1.7E-20 | 1.35 | 5.5E-20 | 1.41 | 1.8E-38 | 0.07 | 39 | HLA-DR/DQ | Novel |
| 6 | 32,767,856 | rs9275224 | G | 0.51 | 0.59 | 1.33 | 1.2E-13 | 1.38 | 5.6E-18 | 1.36 | 5.9E-30 | 0.56 | 0 | HLA-DR/DQ | Known |
| 6 | 32,778,286 | rs2856717 | G | 0.62 | 0.77 | 1.26 | 6.4E-08 | 1.27 | 3.1E-09 | 1.27 | 1.1E-15 | 0.27 | 19 | HLA-DR/DQ | Known |
| 6 | 32,789,609 | rs9275596 | T | 0.65 | 0.80 | 1.43 | 7.7E-15 | 1.46 | 4.1E-18 | 1.44 | 2.5E-31 | 0.09 | 39 | HLA-DR/DQ | Known |
| 6 | 32,919,607 | rs2071543 | G | 0.87 | 0.80 | 1.22 | 2.3E-04 | 1.09 | 8.8E-02 | 1.15 | 1.5E-04 | <0.01 | 76 | TAP2/PSMB9 | Known |
| 6 | 33,194,426 | rs1883414 | G | 0.68 | 0.78 | 1.27 | 1.3E-08 | 1.17 | 1.1E-04 | 1.22 | 1.5E-11 | 0.79 | 0 | HLA-DP | Known |
| 8 | 6,810,195 | rs2738048 | T | 0.69 | 0.68 | 1.05 | 2.1E-01 | 1.12 | 1.6E-04 | 1.10 | 1.6E-04 | 0.04 | 44 | DEFA | Known |
| 8 | 6,887,746 | rs10086568 | A | 0.33 | 0.27 | 1.17 | 1.2E-04 | 1.16 | 2.1E-06 | 1.16 | 1.0E-09 | 0.78 | 0 | DEFA | Novel |
| 9 | 138,386,317 | rs4077515 | T | 0.40 | 0.28 | 1.22 | 4.1E-07 | 1.12 | 1.5E-04 | 1.16 | 1.2E-09 | 0.55 | 0 | CARD9 | Novel |
| 16 | 31,265,261 | rs11150612 | A | 0.36 | 0.75 | 1.21 | 4.4E-06 | 1.17 | 5.1E-07 | 1.18 | 1.3E-11 | 0.57 | 0 | ITGAM-ITGAX | Novel |
| 16 | 31,276,375 | rs11574637 | T | 0.82 | 1.00 | 1.47 | 2.8E-10 | 1.22 | 5.6E-05 | 1.32 | 8.1E-13 | 0.70 | 0 | ITGAM-ITGAX | Novel |
| 17 | 7,403,693 | rs3803800 | A | 0.20 | 0.32 | 1.12 | 1.2E-02 | 1.13 | 2.5E-04 | 1.12 | 9.3E-06 | 0.38 | 7 | TNFSF13 | Known |
| 22 | 28,824,371 | rs2412971 | G | 0.54 | 0.67 | 1.21 | 4.6E-07 | 1.20 | 2.2E-06 | 1.20 | 4.8E-12 | 0.12 | 35 | HORMAD2 | Known |
*
Based on NCBI version 36 (hg-18) genome assembly
**
Only non-redundant SNPs with mutually independent effects are included; the complete list of analyzed SNPs is provided in the Supplementary Table 5.