Table 2.
Association of five novel SLE loci replicated across eight Asian cohorts and a European cohort. KR: Korean, HC: Han Chinese, MC: Malaysian Chinese; JPT: Japanese; SHC: Shanghai Han Chinese; BHC: Beijing Han Chinese; HK: Hong Kong Chinese; European Ancestry cohort (Bentham et al. 2016); Han Chinese replication cohort (Morris et al. 2016); Overall: Meta-analysis of all eight Asian and European cohorts; OR: odds ratio; CI: 95% confidence interval for odds. In the Han Chinese replication cohort for rs11235604, we used MAF and P-value for the proxy SNP rs77971648 which is in LD (D'=1; r2=0.88) with rs11235604. MAF: Minor allele frequency for cases/controls
| SNP (Alleles) | Nearest Gene | MAF/P-value for the discovery cohorts |
Meta P-value OR (95% CI) | MAF/P-value for the replication cohorts |
Overall P-value OR (95% CI) | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| KR | HC | MC | JPT | SHC | BHC | HK | European | Han Chinese | ||||
| rs11235604 (T/C) | ATG16L2 | 0.067/0.099 | 0.092/0.100 | 0.093/0.119 | 0.072/0.088 | 0.083/0.087 | 0.093/0.099 | 1.90E-09 | 0.081/0.091 | monomorphic | 0.076/0.097 | 8.87E-12 |
| 2.69E-09 | 5.19E-01 | 1.71E-01 | 2.45E-02 | 6.98E-01 | 5.87E-01 | 0.76 (0.69-0.84) | 2.07E-01 | 1.78E-3 | 0.78(0.71-0.85) | |||
| rs10936599 (C/T) | MYNN | 0.435/0.389 | 0.492/0.460 | 0.456/0.484 | 0.394/0.363 | 0.489/0.455 | 0.482/0.455 | 4.93E-09 | 0.483/0.452 | 0.783/0.754 | 0.465/0.457 | 1.92E-13 |
| 5.39E-07 | 1.15E-01 | 3.16E-01 | 1.49E-02 | 9.19E-02 | 1.27E-01 | 1.16 (1.10-1.22) | 3.75E-02 | 1.99E-05 | 3.12E-01 | 1.14(1.10-1.18) | ||
| rs223881 (C/T) | CCL22 | 0.455/0.492 | 0.457/0.528 | 0.509/0.587 | 0.362/0.402 | 0.536/0.534 | 0.497/0.506 | 2.06E-08 | 0.538/0.579 | 0.741/0.765 | 0.533/0.567 | 5.87E-16 |
| 9.31E-05 | 1.29E-03 | 7.23E-03 | 2.60E-03 | 9.08E-01 | 5.94E-01 | 0.87 (0.82-0.91) | 1.14E-02 | 6.88E-06 | 5.51E-03 | 0.87(0.84-0.90) | ||
| rs2762340 (G/A) | ANKS1A | 0.341/0.381 | 0.278/0.339 | 0.235/0.279 | 0.348/0.391 | 0.282/0.268 | 0.255/0.291 | 5.05E-07 | 0.234/0.235 | 0.474/0.499 | 0.253/0.277 | 4.93E-15 |
| 3.15E-05 | 7.19E-03 | 1.30E-01 | 6.43E-04 | 4.63E-01 | 2.50E-02 | 0.85 (0.81-0.90) | 9.81E-01 | 3.19E-04 | 1.84E-05 | 0.87(0.84-0.90) | ||
| rs1308020 (T/C) | RNASEH2C | 0.227/0.269 | 0.231/0.235 | 0.210/0.275 | 0.229/0.258 | 0.187/0.262 | 0.217/0.291 | 1.77E-09 | 0.223/0.262 | 0.327/0.344 | 0.219/0.252 | 2.96E-19 |
| 1.17E-07 | 8.80E-01 | 6.45E-03 | 1.34E-02 | 3.46E-05 | 1.23E-05 | 0.78 (0.73-0.83) | 2.49E-03 | 2.32E-03 | 8.28E-03 | 0.84(0.81-0.88) | ||