Table 3.
Meta-analysis results of the five GWASs of gynecologic diseases
| SNPa | Chr | Position (bp)b | Genes | Ref/Altc | Alt Allele Freqd | Imputation Rsq | mach2dat | BOLT-LMM | Novel loci | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| All cases vs controls | RE2C | All cases vs controls | RE2C | ||||||||||||
| OR (95% CI) | P | P | I2 (%)e | OR (95% CI) | P | P | I2 (%)e | ||||||||
| rs7412010 | 1 | 22 436 446 | CDC42, WNT4 | G/C | 0.58 | 0.98 | 1.14 (1.10–1.19) | 2.3 × 10−10 | 4.3 × 10−11 | 77.8 | 1.12 (1.08–1.15) | 5.0 × 10−11 | 3.7 × 10−10 | 91.7 | |
| rs937380553 | 2 | 52 063 361 | LOC730100 | A/G | 0.014 | 0.94 | 1.22 (1.03–1.45) | 2.1 × 10−2 | 8.9 × 10−8 | 83.0 | 1.16 (1.01–1.33) | 3.6 × 10−2 | 2.0 × 10−8 | 77.4 | * |
| rs202217993 | 6 | 29 386 975 | the MHC region | GT/G | 0.10 | 0.95 | 1.20 (1.12–1.28) | 2.7 × 10−7 | 1.8 × 10−8 | 69.2 | 1.18 (1.11–1.25) | 1.2 × 10−8 | 1.8 × 10−9 | 76.2 | |
| rs17179851 | 6 | 29 924 440 | the MHC region | T/C | 0.25 | 0.93 | 1.14 (1.08–1.19) | 8.8 × 10−8 | 9.3 × 10−8 | 44.3 | 1.11 (1.07–1.15) | 6.8 × 10−8 | 6.8 × 10−7 | 74.1 | |
| rs117670375 | 6 | 30 687 472 | the MHC region | C/T | 0.11 | 0.94 | 1.18 (1.10–1.26) | 1.0 × 10−6 | 2.8 × 10−9 | 81.3 | 1.16 (1.10–1.22) | 1.3 × 10−7 | 2.0 × 10−10 | 79.2 | |
| rs12225799 | 11 | 241 124 | BET1L, RIC8A | C/G | 0.13 | 0.99 | 0.78 (0.73–0.84) | 1.5 × 10−13 | 2.1 × 10−15 | 83.7 | 0.81 (0.78–0.86) | 3.3 × 10−16 | 3.7 × 10−17 | 95.3 | |
| rs141244868 | 11 | 244 817 | BET1L, RIC8A | GA/G | 0.13 | 0.98 | 0.78 (0.73–0.84) | 1.9 × 10−13 | 1.6 × 10−15 | 84.0 | 0.81 (0.78–0.86) | 4.7 × 10−16 | 4.2 × 10−17 | 95.3 | |
| rs112251865 | 22 | 40 665 225 | TNRC6B | C/T | 0.36 | 0.99 | 1.12 (1.08–1.17) | 3.0 × 10−8 | 2.3 × 10−9 | 75.5 | 1.10 (1.07–1.14) | 7.6 × 10−9 | 3.3 × 10−8 | 91.4 | |
| rs17332320 | 22 | 40 711 620 | TNRC6B | G/T | 0.36 | 1.00 | 1.12 (1.08–1.17) | 2.4 × 10−8 | 2.9 × 10−7 | 77.3 | 1.10 (1.07–1.14) | 6.7 × 10−9 | 1.5 × 10−8 | 91.6 | |
The underlined odds ratios (OR) and P-values indicate the analytic method which showed the most significant association for each SNP among the four methods, joint analysis of all cases versus shared controls and random-effect meta-analysis using mach2dat and BOLT-LMM, respectively
OR in BOLT-LMM is adjusted using case fraction u, using the formula; log(OR) = β/(u × (1-u)) RE2C does not produce OR
aVariants significantly associated with gynecologic diseases.
bBased on hg19
cReference (Ref) and alternative (Alt) alleles on forward strand
dAlternative allele frequency among control subjects
eI2 statistics were calculated using Metasoft (v2.0.1)