Table 2. Novel SNPs showing genome-wide significance (P = 5×10−8) in SLE following meta-analysis of UK, US, and Swedish cohorts.
| MARKER | Locus | Risk allele | UK population870 cases, 5551 controls | P value (US/SWE)a 3273 cases, 12188 controls | Combined AnalysisFisher's testP value | |||
| Freq risk alleleb | OR | P value | OR | P value | ||||
| rs10911363 | NCF2 | T | 0.27 | 1.23 | 3.02×10−4 | 1.19 | 9.50×10−8 | 2.87×10−11 |
| rs2366293 | IKZF1 | G | 0.14 | 1.20 | 8.77×10−3 | 1.23 | 2.66×10−7 c | 2.33×10−9 |
| rs2280381 | IRF8 | A | 0.62 | 1.11 | 0.0491 | 1.16 | 2.53×10−7 c | 1.24×10−8 |
| rs1990760 | IFIH1 | T | 0.61 | 1.11 | 0.0487 | 1.17 | 3.34×10−7 | 1.63×10−8 |
| rs280519 | TYK2 | A | 0.47 | 1.20 | 5.24×10−4 | 1.16 | 7.40×10−5 d | 3.88×10−8 |
a
For sample numbers see reference [4] and Table S1 (US GWAS: 1310 cases and 7859 controls; US replication cohort: 1129 cases and 2991 controls; Swedish replication cohort: 834 cases and 1388 controls).
b
The risk allele frequency was calculated in control individuals.
c
Unpublished data.
d
The combined P value was calculated from imputed genotypes in the US GWAS dataset and direct genotyping in the US and SWE replication datasets.