Table 2.
Case–control analysis in replication study
| SNP | Position | Allele | MAF−case | MAF−control | OR | (95% CI) | P | P* | |
|---|---|---|---|---|---|---|---|---|---|
| BANK1 | rs17266594 | 102 969 945 | C<T | 0.137 | 0.207 | 0.606 | (0.51–0.72) | 4.67 × 10−9 | 4.15 × 10−5 |
| BANK1 | rs3733197 | 103 058 310 | A<G | 0.204 | 0.234 | 0.838 | (0.72–0.97) | 0.021 | 0.048 |
| BANK1 | *rs4522865 | 102 934 911 | G<A | 0.378 | 0.456 | 0.725 | (0.64–0.82) | 2.93 × 10−3 | 9.12 × 10−3 |
| TNFSF4 | rs2205960 | 171 458 098 | T<G | 0.313 | 0.260 | 1.296 | (1.13–1.49) | 2.41 × 10−4 | 3.87 × 10−3 |
| TNFSF4 | rs844648 | 171 490 486 | A<G | 0.503 | 0.454 | 1.215 | (1.07–1.38) | 2.47 × 10−3 | 0.024 |
Abbreviations: P*, P-values adjusted for age and sex by logistic regression; SNP, single nucleotide polymorphism.
Note that in rs844648, ‘A' is the minor allele (frequency=0.454) in controls, but it becomes the major allele in cases (frequency=0.503); ‘*', all the SNPs were replicated by TaqMan in 949 SLE patients and 1042 controls, except rs4522865, which was replicated by Sequenom in 360 cases and 360 controls.