Table 3.
Validation of selected SNPs on the X chromosome in the central region
| Discovery set (central)a | Central validationb | Meta (discovery + central validation)c | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Marker | Minor allele | Position (Hg19) | Annotation | Gene symbol | PVAL | OR | MAF case | MAF control | PVAL | OR | MAF case | MAF control | PVAL (FE) | PVAL (RE) | OR (FE) | OR (RE) | I 2 | PVAL (Het) |
| rs5914778 | A | 56758231 | Intronic | LINC01420 | 3.59 × 10–3 | 1.29 | 0.286 | 0.238 | 7.15 × 10–7 | 1.33 | 0.296 | 0.24 | 1.00 × 10–8 | 1.00 × 10–8 | 1.32 | 1.32 | 0 | 7.58 × 10–1 |
| rs1527803 | A | 16421982 | 184 kb 3′ of CTPS2 | NA | 6.75 × 10–2 | 0.87 | 0.368 | 0.402 | 1.90 × 10–2 | 1.13 | 0.403 | 0.374 | 3.63 × 10–1 | 9.82 × 10–1 | 1.04 | 1.00 | 87.5 | 4.70 × 10–3 |
| rs5963635 | A | 39166975 | None | LOC286442 | 1.40 × 10–3 | 1.34 | 0.247 | 0.197 | 2.17 × 10–1 | 1.08 | 0.230 | 0.217 | 5.17 × 10–3 | 1.08 × 10–1 | 1.15 | 1.19 | 74.1 | 4.94 × 10–2 |
| rs1860995 | G | 119502122 | Intronic | ATP1B4 | 7.48 × 10–4 | 1.30 | 0.417 | 0.355 | 6.74 × 10–1 | 1.02 | 0.395 | 0.389 | 1.69 × 10–2 | 2.87 × 10–1 | 1.10 | 1.11 | 81.4 | 4.33 × 10–2 |
| rs2536576 | G | 147417249 | 165 kb 5′ of AFF2 | NA | 5.73 × 10–3 | 1.34 | 0.172 | 0.134 | 9.43 × 10–1 | 1.01 | 0.152 | 0.152 | 1.12 × 10–1 | 3.36 × 10–1 | 1.10 | 1.15 | 80.2 | 2.45 × 10–2 |
| rs17326228 | G | 106239318 | Intronic | MORC4 | 2.56 × 10–4 | 1.33 | 0.438 | 0.370 | 3.01 × 10–1 | 0.95 | 0.418 | 0.432 | 3.82 × 10–1 | 6.14 × 10–1 | 1.02 | 1.05 | 88.5 | 1.75 × 10–3 |
| rs17329976 | G | 142130195 | 8.1 KB 3′ of SPANXN4 | NA | 4.28 × 10–2 | 0.83 | 0.179 | 0.209 | 1.58 × 10–1 | 0.91 | 0.160 | 0.174 | 2.23 × 10–2 | 3.62 × 10–2 | 0.85 | 0.83 | 51.6 | 1.62 × 10–1 |
| rs5936901 | G | 67975499 | 30 kb 3′ of STARD8 | NA | 4.45 × 10–4 | 1.33 | 0.371 | 0.308 | 5.53 × 10–1 | 0.97 | 0.342 | 0.350 | 1.28 × 10–1 | 4.50 × 10–1 | 1.07 | 1.13 | 90.3 | 1.30 × 10–3 |
| rs10218247 | A | 83476018 | 33 kb 5′ of RPS6KA6 | NA | 3.67 × 10–3 | 0.78 | 0.241 | 0.289 | 5.47 × 10–1 | 0.96 | 0.248 | 0.255 | 2.85 × 10–2 | 3.06 × 10–1 | 0.91 | 0.86 | 82.4 | 1.24 × 10–2 |
| rs5970959 | G | 22987793 | 30 kb 5′ of DDX53 | DDX53 | 1.42 × 10–2 | 1.25 | 0.254 | 0.215 | 1.57 × 10–1 | 0.92 | 0.251 | 0.267 | 3.76 × 10–1 | 6.41 × 10–1 | 1.03 | 1.05 | 86.7 | 2.06 × 10–3 |
| rs6631753 | A | 33199451 | Intronic | DMD | 6.94 × 10–3 | 0.81 | 0.376 | 0.426 | 5.09 × 10–1 | 1.04 | 0.374 | 0.366 | 7.12 × 10–2 | 4.69 × 10–1 | 0.93 | 0.91 | 89.2 | 4.35 × 10–3 |
| rs2411864 | G | 16377763 | 206 kb 3′ of GRPR | NA | 5.04 × 10–3 | 0.76 | 0.154 | 0.194 | 4.81 × 10–1 | 1.05 | 0.165 | 0.159 | 2.98 × 10–1 | 5.16 × 10–1 | 0.94 | 0.90 | 86.2 | 7.10 × 10–3 |
aFrom Han et al. [13] with 1017 cases and 539 controls from central China
bConsists of 1156 cases and 2330 controls
cConsists of 2173 cases and 2869 controls
FE fixed effects, Het heterogeneity, I 2 heterogeneity statistic, MAF minor allele frequency, NA not available, OR odds ratio, PVAL P value, RE random effects, SNP single nucleotide polymorphism