Table 2. SNPs genotyped in phase 3 and summary description from the meta-analysis of all available data.
All samples |
Replication samples |
Replication samples of European ancestry |
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SNP | Rank | Chr. | Position | Variant | Number of sets | Pheta | l2 (%) | Effects model | P | OR (95% CI) |
Number of sets | Pheta | l2 (%) | Effects model | P | OR (95% CI) |
Number of sets | Pheta | l2 (%) | Effects model | P | OR (95% CI) |
rs6533603b | 3 | 4 | 113440251 | T | 9 | 0.001 | 68 | Random | 0.81 | 1.01 (0.95-1.07) |
8 | 0.36 | 9 | Fixed | 0.21 | 0.98 (0.94-1.01) |
7 | 0.44 | 0 | Fixed | 0.48 | 0.99 (0.95-1.03) |
rs7014346b | 1 | 8 | 128493974 | A | 9 | 0.343 | 11 | Fixed | 8.60 × 10-26 | 1.19 (1.15-1.23) |
8 | 0.26 | 21 | Fixed | 1.85 × 10-20 | 1.19 (1.14-1.23) |
7 | 0.18 | 32 | Fixed | 4.44 × 10-16 | 1.19 (1.14-1.24) |
rs7842552 | 8 | 128500876 | G | 8 | 0.026 | 56 | Random | 1.20 × 10-5 | 1.15 (1.08-1.23) |
7 | 0.02 | 59 | Random | 4.48 × 10-4 | 1.14 (1.06-1.23) |
6 | 0.01 | 65 | Random | 1.85 × 10-3 | 1.15 (1.05-1.25) |
|
rs11213809 | 4 | 11 | 110640955 | A | 8 | 0.086 | 43 | Fixed | 7.93 × 10-8 | 1.11 (1.07-1.16) |
7 | 0.29 | 18 | Fixed | 6.79 × 10-4 | 1.08 (1.03-1.13) |
6 | 0.34 | 11 | Fixed | 2.98 × 10-4 | 1.09 (1.04-1.14) |
rs3802842b | 11 | 110676919 | C | 9 | 0.050 | 48 | Fixed | 5.82 × 10-10 | 1.11 (1.08-1.15) |
8 | 0.18 | 32 | Fixed | 5.54 × 10-6 | 1.09 (1.05-1.13) |
7 | 0.43 | 0 | Fixed | 7.82 × 10-7 | 1.12 (1.07-1.17) |
|
rs7947952 | 11 | 110686330 | T | 3 | 0.081 | 60 | Fixed | 0.04 | 1.06 (1.00-1.11) |
2 | 0.12 | 58 | Fixed | 0.81 | 1.01 (0.94-1.09) |
1 | - | - | - | 0.19 | 1.08 (0.96-1.21) |
|
rs10749971 | 11 | 110694368 | G | 8 | 0.818 | 0 | Fixed | 6.71 × 10-6 | 1.09 (1.05-1.13) |
7 | 0.86 | 0 | Fixed | 9.46 × 10-4 | 1.08 (1.03-1.13) |
6 | 0.83 | 0 | Fixed | 7.67 × 10-4 | 1.08 (1.03-1.13) |
|
rs4514461 | 11 | 110732153 | A | 8 | 0.072 | 46 | Fixed | 7.90 × 10-3 | 1.05 (1.01-1.09) |
7 | 0.20 | 30 | Fixed | 0.19 | 1.03 (0.99-1.07) |
6 | 0.21 | 30 | Fixed | 0.096 | 1.04 (0.99-1.09) |
|
rs12799202 | 11 | 110749966 | G | 8 | 0.533 | 0 | Fixed | 4.98 × 10-4 | 1.07 (1.03-1.12) |
7 | 0.55 | 0 | Fixed | 0.01 | 1.06 (1.01-1.11) |
6 | 0.73 | 0 | Fixed | 0.003 | 1.08 (1.03-1.14) |
|
rs4939827b | 2 | 18 | 44707461 | T | 9 | 0.336 | 12 | Fixed | 7.77 × 10-28 | 1.20 (1.16-1.24) |
8 | 0.25 | 22 | Fixed | 4.38 × 10-23 | 1.20 (1.16-1.24) |
7 | 0.17 | 33 | Fixed | 8.70 × 10-19 | 1.20 (1.15-1.25) |
rs12953717 | 18 | 44707927 | T | 4 | 0.964 | 0 | Fixed | 3.10 × 10-11 | 1.18 (1.12-1.23) |
3 | 0.93 | 0 | Fixed | 2.07 × 10-7 | 1.18 (1.11-1.26) |
2 | 0.71 | 0 | Fixed | 0.002 | 1.18 (1.06-1.30) |
|
rs9951602b | 5 | 18 | 74758767 | T | 9 | 0.059 | 47 | Fixed | 0.44 | 1.02 (0.97-1.07) |
8 | 0.04 | 53 | Random | 0.64 | 1.02 (0.94-1.10) |
7 | 0.03 | 56 | Random | 0.51 | 1.03 (0.94-1.13) |
The Mantel-Haenzsel method was used.
When there was no significant heterogeneity (Phet > 0.05), the Mantel-Haenszel method was used to estimate pooled allelic effects under a fixed effect model, A random effects model, the DerSimonian-Laird method, was used if there was significant heterogeneity.
SNPs identified through the GWAS.