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Table 3 Validation of selected SNPs on the X chromosome in the central region

From: Discovery of a novel genetic susceptibility locus on X chromosome for systemic lupus erythematosus

  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
  1. aFrom Han et al. [13] with 1017 cases and 539 controls from central China
  2. bConsists of 1156 cases and 2330 controls
  3. cConsists of 2173 cases and 2869 controls
  4. 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