List of the six NKAPL locus SNPs showing the most significant association with rheumatoid arthritis in the Toronto- and Halifax-based case/control cohorts.
| RAF | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| SNP | Gene | Risk allele | Sample cohort | Case | Control | OR (95% CI) | p Value* | PFDR value | Cochran Q p value† |
| rs13195291 | ZNF193 | A | Toronto | 0.115 | 0.075 | 1.61 (1.33 to 1.94) | 5.03×10−7 | 8.60×10−6 | |
| Halifax | 0.116 | 0.086 | 1.40 (1.04 to 1.89) | 0.03 | 0.04 | ||||
| Combined† | 0.116 | 0.077 | 1.56 (1.33 to 1.82) | 2.79×10−8 | 4.20×10−8 | 0.45 | |||
| rs35656932 | ZNF193 | T | Toronto | 0.118 | 0.075 | 1.66 (1.38 to 1.99) | 3.82×10−8 | 1.80×10−6 | |
| Halifax | 0.119 | 0.083 | 1.48 (1.11 to 1.99) | 8.31×10−3 | 0.02 | ||||
| Combined | 0.118 | 0.075 | 1.62 (1.39 to 1.89) | 7.34×10−10 | 2.20×10−9 | 0.52 | |||
| rs13204012 | ZNF193 | A | Toronto | 0.116 | 0.075 | 1.63 (1.35 to 1.95) | 1.53×10−7 | 3.90×10−6 | |
| Halifax | 0.11 | 0.088 | 1.29 (0.96 to 1.74) | 0.09 | 0.10 | ||||
| Combined | 0.114 | 0.078 | 1.53 (1.31 to 1.79) | 5.66×10−8 | 5.60×10−8 | 0.20 | |||
| rs17720293 | ZNF307 | T | Toronto | 0.135 | 0.089 | 1.60 (1.35 to 1.90) | 5.27×10−8 | 1.80×10−6 | |
| Halifax | 0.129 | 0.107 | 1.23 (0.94 to 1.60) | 0.139 | 0.14 | ||||
| Combined | 0.133 | 0.093 | 1.49 (1.29 to 1.72) | 4.29×10−8 | 5.10×10−8 | 0.10 | |||
| rs13208096 | NKAPL | G | Toronto | 0.115 | 0.075 | 1.61(1.34 to 1.94) | 3.69×10−7 | 7.50×10−6 | |
| Halifax | 0.116 | 0.081 | 1.48 (1.10 to 1.99) | 8.75×10−3 | 0.02 | ||||
| Combined | 0.115 | 0.076 | 1.58 (1.35 to 1.85) | 6.99×10−9 | 1.40×10−8 | 0.64 | |||
| rs67998226 | ZNF187 | C | Toronto | 0.122 | 0.077 | 1.66 (1.39 to 1.99) | 2.48×10−8 | 1.80×10−6 | |
| Halifax | 0.122 | 0.086 | 1.47 (1.10 to 1.97) | 9.88×10−3 | 0.02 | ||||
| Combined | 0.122 | 0.079 | 1.62 (1.39 to 1.88) | 6.53×10−10 | 2.20×10−9 | 0.48 | |||
Genotype data are shown for six SNPs tested in 1368 cases and 1471 controls from Toronto in step 1 and replication in 710 cases and 430 controls from Halifax in step 2. Data for all other SNPs tested in Toronto cohort are shown in online supplementary table S1.
*Nominal p value from an allele-based case-control comparison with 1 degree of freedom; p<0.05 are highlighted in bold type. PFDR corresponds to p values adjusted for multiple testing using the False Discovery Method implemented in PLINK.
†Genotyping data from the Toronto and Halifax cohorts were merged in PLINK and combined PCan values for association evaluated using Cochran-Mantel Haenszel tests and the Cochran Q test for heterogeneity.
FDR, False Discovery Rate; NKAPL, NF-κB activating protein-like; RAF, risk allele frequency.