Table 2.
Association of the top hits of stage 1 and stage 2 in East Asians
| SNP | Gene | Chr | Base pair position | Alleles | Stage | Risk allele frequency | Effect (SE) | P value | n |
|---|---|---|---|---|---|---|---|---|---|
| Novel loci | |||||||||
| rs6684514* | TMEM79 | 1 | 154,522,080 | G/A | 1 | 0.75 | 0.09 (0.01) | 1.1E-15 | 20,831 |
| 2 | 0.78 | 0.09 (0.02) | 2.1E-09 | 9,494 | |||||
| 1+2 | 0.76 | 0.09 (0.01) | 1.3E-23 | 30,325 | |||||
| rs9399137* | HBS1L/MYB | 6 | 135,460,711 | T/C | 1 | 0.72 | 0.06 (0.01) | 1.9E-08 | 20,535 |
| 2 | 0.65 | 0.07 (0.01) | 7.6E-08 | 9,501 | |||||
| 1+2 | 0.69 | 0.07 (0.01) | 8.5E-15 | 30,036 | |||||
| rs1467311 | 9q31.2 | 9 | 109,576,753 | G/A | 1 | 0.22 | 0.07 (0.01) | 2.9E-08 | 20,845 |
| 2 | 0.24 | 0.01 (0.01) | 3.5E-01 | 11,474 | |||||
| 1+2 | 0.23 | 0.04 (0.01) | 1.0E-06 | 32,319 | |||||
| rs540078 | PSMD13 | 11 | 244,256 | T/C | 1 | 0.46 | 0.04 (0.01) | 6.2E-06 | 20,865 |
| 2 | 0.39 | 0.01 (0.01) | 4.1E-01 | 9,485 | |||||
| 1+2 | 0.44 | 0.03 (0.01) | 3.2E-05 | 30,350 | |||||
| rs174570 | FADS2 | 11 | 61,353,788 | C/T | 1 | 0.52 | 0.05 (0.01) | 5.4E-07 | 20,639 |
| 2 | 0.59 | 0.03 (0.01) | 3.8E-02 | 11,524 | |||||
| 1+2 | 0.55 | 0.04 (0.01) | 2.0E-07 | 32,163 | |||||
| rs9933309* | CYBA | 16 | 87,372,433 | C/T | 1 | 0.64 | 0.08 (0.01) | 3.3E-08 | 11,015 |
| 2 | 0.63 | 0.05 (0.03) | 1.1E-01 | 1,983 | |||||
| 1+2 | 0.63 | 0.07 (0.01) | 1.1E-08 | 12,998 | |||||
| rs11667918* | MYO9B | 19 | 17,093,499 | C/T | 1 | 0.61 | 0.06 (0.01) | 1.9E-10 | 20,835 |
| 2 | 0.65 | 0.04 (0.01) | 3.7E-03 | 9,516 | |||||
| 1+2 | 0.62 | 0.06 (0.01) | 9.0E-12 | 30,351 | |||||
| Known loci | |||||||||
| rs3755157* | G6PC2/ABCB11 | 2 | 169,500,417 | T/C | 1 | 0.34 | 0.07 (0.01) | 2.8E-11 | 20,630 |
| rs7772603* | CDKAL1 | 6 | 20,773,925 | C/T | 1 | 0.42 | 0.06 (0.01) | 3.5E-08 | 19,156 |
| rs1799884* | GCK | 7 | 44,195,593 | T/C | 1 | 0.19 | 0.12 (0.01) | 1.5E-22 | 20,874 |
| rs4737009* | ANK1 | 8 | 41,749,562 | A/G | 1 | 0.50 | 0.09 (0.01) | 1.3E-15 | 20,558 |
| 2 | 0.54 | 0.05 (0.03) | 1.4E-01 | 1,984 | |||||
| 1+2 | 0.51 | 0.08 (0.01) | 1.1E-15 | 22,542 | |||||
| rs1046875* | FN3K | 17 | 78,278,715 | A/G | 1 | 0.49 | 0.08 (0.01) | 1.6E-14 | 20,871 |
| 2 | 0.52 | 0.11 (0.03) | 2.6E-04 | 1,984 | |||||
| 1+2 | 0.49 | 0.08 (0.01) | 3.8E-17 | 22,855 |
The index SNPs were grouped into novel loci that were first discovered in our study and known loci that have been reported in previous publications. Gene refers to the most relevant gene within each locus. The cytoband of 9q31.2 was designated to rs1467311 since no gene was found in the 400 Kb flanking region nearby. Alleles are given as the effect allele/other allele. Effect and SE are the risk and its SE, respectively. For the novel loci, association result were given for the stage 1, stage 2, and the meta-analyzed stage 1 and stage 2, indicated as 1, 2, and 1+2, respectively. Chr, chromosome number.
*The index SNPs showed genome-wide significance in stage 1.