Table 2.
Summary of the exome-array meta-analysis and replication results for markers with P < 1 × 10–4 in analysis including ‘All’ endometriosis cases. Chr, Chromosome; Genomic position is shown relative to GRCh37 (hg19); NS, nonsynonymous; EA, effect allele; NEA, non-effect allele; EAF, average effect allele frequency in the discovery cohorts; OR, odds ratio with respect to EA; CI, confidence interval; P het, P-value from heterogeneity test; P RE2, P-value from the Han Eskin random-effects (RE2) model.
| Chr | dbSNP ID | Position (bp) | Functional region | Genes | EA | NEA | Exome-array meta-analysis (all) | deCODE replication (all) | Total association analysis (all) | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| EAF | OR (95% CI) | P | P het | P RE2 | OR (95% CI) | P | OR (95% CI) | P | P het | P RE2 | |||||||
| 10 | rs1801232 | 16870912 | NS | CUBN | T | G | 0.08 | 0.82 (0.76–0.89) | 7.47 × 10–7 | 0.25 | 0.95 (0.84–1.07) | 0.37 | 0.86 (0.80–0.92) | 4.18 × 10−6 | 0.09 | 5.97 × 10–6 | |
| 2 | rs6542095 | 113529183 | intergenic | IL1A | T | C | 0.69 | 0.89 (0.85–0.94) | 1.71 × 10–6 | 0.75 | 0.93 (0.86–1.01) | 0.07 | 0.90 (0.87–0.94) | 4.39 × 10−7 | 0.76 | ||
| 7 | rs17172694 | 46437154 | intergenic | IGFBP3 | T | G | 0.08 | 1.21 (1.11–1.30) | 3.27 × 10−6 | 0.52 | 1.11 (0.99–1.25) | 0.09 | 1.18 (1.10–1.26) | 1.33 × 10−6 | 0.48 | ||
| 16 | rs78108426 | 11001421 | NS | CIITA | A | C | 0.01 | 1.87 (1.40–2.49) | 1.90 × 10−5 | 0.07 | 2.40 × 10−5 | 0.34 (0.11–1.05) | 0.06 | 1.68 (1.28–2.22) | 2.31 × 10−4 | 0.004 | 6.99 × 10−5 |
| 10 | rs138680811 | 98157006 | NS | TLL2 | A | G | 0.003 | 2.44 (1.61–3.71) | 2.72 × 10−5 | 0.40 | 1.96 (0.88–4.40) | 0.10 | 2.33 (1.61–3.38) | 7.49 × 10−6 | 0.53 | ||
| 2 | rs17261772 | 135911422 | synonymous | RAB3GAP1 | T | C | 0.74 | 0.88 (0.83–0.94) | 3.33 × 10−5 | 0.0007 | 1.27 × 10−6 | 1.02 (0.91–1.14) | 0.78 | 0.91 (0.86–0.96) | 4.20 × 10−4 | 0.0002 | 3.87 × 10−6 |
| 10 | rs12777823 | 96405502 | intergenic | CYP2C18 | A | G | 0.15 | 1.13 (1.07–1.20) | 3.39 × 10−5 | 0.15 | 0.99 (0.89–1.11) | 0.88 | 1.10 (1.05–1.16) | 3.08 × 10−4 | 0.05 | 1.58 × 10−4 | |
| 4 | rs4647930 | 1018705 | NS | FGFRL1 | A | C | 0.27 | 0.90 (0.86–0.95) | 3.98 × 10−5 | 0.10 | 1.04 (0.96–1.13) | 0.31 | 0.94 (0.90–0.98) | 2.83 × 10−3 | 0.004 | 3.27 × 10−4 | |
| 16 | rs1639150 | 3747204 | intronic | TRAP1 | T | C | 0.43 | 0.91 (0.88–0.95) | 4.25 × 10−5 | 0.92 | 1.04 (0.97–1.12) | 0.32 | 0.94 (0.91–0.98) | 2.54 × 10−3 | 0.09 | 1.61 × 10−3 | |
| 17 | rs2278868 | 46262171 | NS | SKAP1 | T | C | 0.61 | 1.10 (1.05–1.14) | 4.38 × 10−5 | 0.35 | 1.07 (1.00–1.16) | 0.07 | 1.09 (1.05–1.13) | 8.73 × 10−6 | 0.45 | ||
| 2 | rs114242502 | 235951001 | NS | SH3BP4 | A | G | 0.00 | 5.62 (2.45–12.89) | 4.53 × 10−5 | 0.002 | 5.61 × 10−6 | 2.76 (0.07–115.4) | 0.59 | 5.44 (2.42–12.22) | 4.18 × 10−5 | 0.01 | 6.49 × 10−6 |
| 3 | rs3772836 | 124535635 | intronic | ITGB5 | A | C | 0.04 | 0.80 (0.72–0.89) | 4.70 × 10−5 | 0.29 | 1.13 (0.96–1.34) | 0.15 | 0.89 (0.81–0.97) | 9.11 × 10−3 | 0.005 | 5.21 × 10−4 | |
| 2 | rs13394619 | 11727507 | splicing | GREB1 | A | G | 0.48 | 0.92 (0.88–0.96) | 5.77 × 10−5 | 0.61 | 0.83 (0.77–0.90) | 7.43 × 10−7 | 0.89 (0.86–0.93) | 2.33 × 10−9 | 0.17 | ||
| 9 | rs512110 | 79320640 | NS | PRUNE2 | T | C | 0.76 | 1.11 (1.05–1.16) | 6.61 × 10−5 | 0.71 | 1.04 (0.95–1.13) | 0.38 | 1.09 (1.04–1.14) | 1.04 × 10−4 | 0.59 | ||
| 12 | rs12313736 | 26383959 | NS | SSPN | A | G | 0.04 | 1.25 (1.12–1.39) | 6.73 × 10−5 | 0.70 | 1.05 (0.86–1.30) | 0.63 | 1.20 (1.09–1.32) | 1.67 × 10−4 | 0.53 | ||
| 6 | rs9354308 | 66565353 | intergenic | SLC25A51P1 | A | G | 0.63 | 0.91 (0.87–0.96) | 6.88 × 10−5 | 0.94 | 0.92 (0.86–0.99) | 0.03 | 0.92 (0.88–0.95) | 6.69 × 10−6 | 0.98 | ||
| 10 | rs12767583 | 96547463 | intronic | CYP2C19 | T | C | 0.15 | 1.13 (1.06–1.20) | 7.07 × 10−5 | 0.54 | 0.98 (0.88–1.10) | 0.77 | 1.10 (1.04–1.15) | 6.97 × 10−4 | 0.19 | ||
| 4 | rs11131511 | 64933220 | intergenic | LPHN3-AS1 | T | G | 0.54 | 1.09 (1.05–1.14) | 7.24 × 10−5 | 0.30 | 0.95 (0.89–1.03) | 0.21 | 1.05 (1.02–1.09) | 6.08 × 10−3 | 0.01 | 1.08 × 10−3 | |
| 2 | rs1446585 | 136407479 | intronic | R3HDM1 | A | G | 0.70 | 0.89 (0.84–0.94) | 8.08 × 10−5 | 0.001 | 4.63 × 10−6 | 0.98 (0.89–1.09) | 0.73 | 0.91 (0.87–0.96) | 3.04 × 10−4 | 0.001 | 1.13 × 10−5 |
| 12 | rs12313670 | 26383834 | NS | SSPN | A | G | 0.04 | 1.24 (1.12–1.38) | 8.42 × 10−5 | 0.75 | 1.05 (0.85–1.30) | 0.63 | 1.20 (1.09–1.32) | 1.96 × 10−4 | 0.59 | ||
| 10 | rs1126545 | 96493058 | NS | CYP2C18 | T | C | 0.15 | 1.13 (1.06–1.19) | 8.51 × 10−5 | 0.60 | 0.98 (0.88–1.10) | 0.76 | 1.09 (1.04–1.15) | 8.53 × 10−4 | 0.21 | ||
| 22 | rs148613283 | 18301508 | NS | MICAL3 | T | C | 0.99 | 1.68 (1.29–2.17) | 9.04 × 10−5 | 0.40 | 1.17 (0.68–2.01) | 0.58 | 1.57 (1.24–1.98) | 1.61 × 10−4 | 0.37 | ||