Table 2.
Newly discovered SLE risk loci in the combined dataset
| SNP | Chr. | Critical region |
P |
Gene of interest | Risk allele | Risk allele frequency | OR (95% CI) | |||
|---|---|---|---|---|---|---|---|---|---|---|
| GWAS | US | Sweden | Combined | |||||||
| Genome-wide significant loci | ||||||||||
| rs7708392a | 5 | 150.419–150.441 | 4.5 × 10−7 | 7.7 × 10−4 | 1.2 × 10−5 | 3.8 × 10−13 | TNIP1 | C | 0.24 | 1.27 (1.10–1.35) |
| rs6568431 | 6 | 106.675–106.705 | 6.1 × 10−6 | 0.0016 | 0.0050 | 7.1 × 10−10 | PRDM1 | A | 0.38 | 1.20 (1.14–1.27) |
| rs849142a | 7 | 28.108–28.223 | 4.5 × 10−7 | 0.10 | 5.4 × 10−4 | 1.5 × 10−9 | JAZF1 | T | 0.49 | 1.19 (1.13–1.26) |
| rs11755393a | 6 | 34.658–35.090 | 0.0014 | 3.7 × 10−4 | 5.1 × 10−4 | 2.2 × 10−8 | UHRF1BP1 | G | 0.35 | 1.17 (1.10–1.24) |
| rs3024505 | 1 | 205.007–205.016 | 2.6 × 10−6 | 0.062 | 1.8 × 10−4 | 4.0 × 10−8 | IL10 | A | 0.16 | 1.19 (1.11–1.28) |
| Loci with combined P value < 1 × 10−6 | ||||||||||
| rs10911363a | 1 | 181.672–181.816 | 2.0 × 10−4 | 1.5 × 10−5 | 0.52 | 9.5 × 10−8 | NCF2 | T | 0.27 | 1.19 (1.12–1.26) |
| rs12444486a | 16 | 84.548–84.576 | 3.5 × 10−5 | 0.021 | 0.026 | 1.9 × 10−7 | IRF8 | T | 0.50 | 1.16 (1.10–1.23) |
| rs11013210a | 10 | 23.181–23.337 | 1.6 × 10−5 | 0.013 | 0.12 | 2.0 × 10−7 | ARMC3 | T | 0.21 | 1.18 (1.11–1.26) |
| rs1874791a | 1 | 67.563–67.687 | 3.1 × 10−5 | 0.012 | 0.11 | 3.4 × 10−7 | IL12RB2 | A | 0.18 | 1.18 (1.10–1.26) |
| rs9782955 | 1 | 233.893–234.107 | 6.4 × 10−6 | 0.057 | 0.12 | 4.6 × 10−7 | LYST | C | 0.74 | 1.18 (1.11–1.26) |
| rs7683537a | 4 | 185.805–185.914 | 1.6 × 10−4 | 0.11 | 0.0013 | 7.6 × 10−7 | MLF1IP | T | 0.82 | 1.23 (1.14–1.33) |
| rs428073 | 12 | 117.706–117.315 | 1.7 × 10−5 | 0.22 | 0.0079 | 7.7 × 10−7 | TAOK3 | T | 0.69 | 1.18 (1.11–1.26) |
| rs497273a | 12 | 119.610–119.891 | 5.0 × 10−5 | 0.068 | 0.021 | 8.2 × 10−7 | SPPL3 | G | 0.65 | 1.14 (1.08–1.21) |
| Loci with combined P value < 1 × 10−5 | ||||||||||
| rs1861525 | 7 | 25.097–25.183 | 8.5 × 10−5 | 0.16 | 0.0027 | 1.9 × 10−6 | CYCS | G | 0.05 | 1.27 (1.12–1.45) |
| rs921916 | 7 | 50.193–50.205 | 4.8 × 10−4 | 0.027 | 0.014 | 2.0 × 10−6 | IKZF1 | C | 0.18 | 1.15 (1.07–1.23) |
| rs7333671 | 13 | 73.177–73.198 | 2.2 × 10−4 | 0.14 | 0.0027 | 2.2 × 10−6 | KLF12 | G | 0.08 | 1.22 (1.11–1.34) |
| rs12992463 | 2 | 22.312–22.464 | 2.1 × 10−5 | 0.23 | 0.023 | 2.6 × 10−6 | – | A | 0.50 | 1.12 (1.06–1.19) |
| rs12620999 | 2 | 237.616–237.770 | 1.6 × 10−5 | 0.040 | 0.45 | 3.1 × 10−6 | COPS8 | C | 0.19 | 1.13 (1.06–1.21) |
| rs503425a | 11 | 118.079–118.198 | 0.0012 | 3.3 × 10−4 | 0.43 | 3.3 × 10−6 | DDX6 | C | 0.20 | 1.16 (1.08–1.24) |
| rs10742326a | 11 | 34.733–34.809 | 1.4 × 10−4 | 0.017 | 0.21 | 3.6 × 10−6 | APIP | G | 0.59 | 1.14 (1.08–1.21) |
| rs4766921a | 12 | 117.835–117.883 | 4.6 × 10−5 | n.a. | 0.036 | 4.6 × 10−6 | KIAA1853 | G | 0.67 | 1.18 (1.09–1.27) |
| rs11951576a | 5 | 6.741–6.866 | 2.5 × 10−5 | 0.42 | 0.014 | 4.6 × 10−6 | POLS-SRD5A | C | 0.69 | 1.14 (1.08–1.22) |
| rs6438700 | 3 | 123.355–123.454 | 7.4 × 10−5 | 0.23 | 0.020 | 5.5 × 10−6 | CD86 | C | 0.82 | 1.18 (1.09–1.27) |
| rs6486730a | 12 | 127.830–127.840 | 8.2 × 10−5 | 0.16 | 0.049 | 6.9 × 10−6 | SLC15A4 | G | 0.41 | 1.13 (1.07–1.19) |
| rs4748857a | 10 | 23.529–23.654 | 2.2 × 10−4 | 0.68 | 1.3 × 10−4 | 6.9 × 10−6 | C10orf67 | C | 0.73 | 1.16 (1.09–1.24) |
| rs3914167a | 5 | 39.426–39.454 | 1.8 × 10−4 | 0.24 | 0.0081 | 7.6 × 10−6 | DAB2-C9 | G | 0.27 | 1.15 (1.09–1.23) |
Samples, critical region, P values, risk alleles and ORs are as defined in the Table 1 legend.
a
Indicates markers that were imputed, as described in Online Methods, from the GWAS samples and directly genotyped in the replication samples. See Supplementary Table 2 for expanded summary statistics.