Table 1. Summary of association results.
We analyzed the top 147 SNPs of the GWAS (including typed and imputed genotypes) in three independent PsV case-control panels (B through D). Data is shown for the seven SNPs that were nominal significant in the combined replication analysis of panels B through D (replication stage P<0.05, highlighted in bold) with consistent direction of effects in panel A and B. The number of cases and controls of each panel is shown in the top column. Results of all 147 SNPs are shown in Supplementary Table 2. SNPs are ranked according to their P value obtained in the GWAS. Nucleotide positions refer to NCBI build 36. Chr., chromosome. A1 denotes the minor allele and A2 is the common allele. Allele frequencies of A1 are shown (AFA1). The P value, the odds ratio (OR) and the 95% CI for carriership of the minor allele A1 are shown for the genome-wide association analysis (panel A). The combined P value of the meta-analysis is shown for the independent replication panels B through D (Prepl.) as well as for the GWAS panel together with the independent replication panels (panels A through D; Pcomb.). rs13210247 was additionally tested in replication panels E and F. Results for this SNP in panels B through F (replication; 6,015 cases and 6,891 controls) and panels A through F (GWAS and replication; 6,487 cases and 8,037 controls) are provided in the main text and in Table 2.
| Panel A – GWAS Germany 472 cases 1146 controls |
Panel B Germany 681cases 1824 controls |
Panel C CASP 1303 cases 1322 controls |
Panel D Genizon 762 cases 994 controls |
Panel B – D (replication only) Combined analysis 2746 cases 4140 controls |
Panel A – D (GWAS & replication) Combined analysis 3218 cases 5286 controls |
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Chr Pos. (bp) |
dbSNP ID | Nearby genes (relative position) |
A1 A2 |
AFA1 Case |
AFA1 Control |
P-value | OR (95% CI) |
AFA1 Case |
AFA1 Control |
AFA1 Case |
AFA1 Control |
AFA1 Case |
AFA1 Control |
Prepl. | Pcomb. |
| 5 158,692,478 |
rs2546890 | IL12B (−2.5 kb) | G A |
0.36 | 0.46 | 8.83×10−08 | 0.65 (0.56–0.76) | 0.38 | 0.44 | 0.42 | 0.49 | 0.45 | 0.53 | 9.07×10−15 | 1.29×10−20 |
| 1 235,345,148 |
rs2485558 | RYR2 (intronic) | G C |
0.31 | 0.24 | 2.81×10−06 | 1.49 (1.26–1.76) | 0.24 | 0.23 | 0.23 | 0.21 | 0.26 | 0.24 | 0.01 | 1.53×10−05 |
| 5 158,705,160 |
rs953861 | IL12B (−15 kb) | G A |
0.23 | 0.17 | 1.60×10−05 | 1.51 (1.25–1.82) | 0.22 | 0.18 | 0.22 | 0.17 | 0.21 | 0.14 | 6.50×10−14 | 6.21×10−18 |
| 14 34,908,987 |
rs2145623 | NFKBIA (+31 kb) | C G |
0.34 | 0.27 | 3.01×10−05 | 1.41 (1.2–1.66) | 0.33 | 0.30 | 0.30 | 0.28 | 0.28 | 0.26 | 2.29×10−03 | 5.01×10−06 |
| 6 112,029,413 |
rs13210247 | TRAF3IP2 (intronic) | G A |
0.10 | 0.06 | 8.17×10−05 | 1.7 (1.3–2.22) | 0.09 | 0.07 | 0.09 | 0.07 | 0.09 | 0.07 | 6.25×10−06 | 7.31×10−09 |
| 7 154,099,909 |
rs916514 | DPP6 (intronic) | G A |
0.09 | 0.14 | 1.37×10−04 | 0.61 (0.47–0.79) | 0.09 | 0.11 | 0.09 | 0.11 | 0.10 | 0.09 | 0.0496 | 6.03×10−04 |
| 11 102,081,585 |
rs1939015 | MMP27 (missense) | G A |
0.12 | 0.16 | 1.56×10−03 | 0.69 (0.55–0.87) | 0.14 | 0.14 | 0.15 | 0.17 | 0.17 | 0.20 | 0.026 | 7.09×10−04 |