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Table 1 Meta-analysis of 66 GWAS-genotyped SNPs in scleroderma (SSc) patients and healthy controls of Caucasian origin

From: A genome-wide association study follow-up suggests a possible role for PPARG in systemic sclerosis susceptibility

Chr Locus SNP Minor/major MAF cases MAF controls P MH OR (CI 95%)a P BD
3 PPARG rs310746 C/T 0.108 0.086 1.90E-06 1.28 [1.12-1.47] 0.33
4 CHRNA9 | RHOH rs6832151 G/T 0.315 0.281 4.30E-06 1.17 [1.075-1.27] 0.05
2 DYSF rs11692280 A/G 0.195 0.220 2.31E-04 0.86 [0.80-0.93] 0.04
4 PGDS rs17021463 T/G 0.393 0.421 2.45E-04 0.89 [0.83-0.94] 0.13
22 DGCR6 rs2543958 G/T 0.127 0.109 4.98E-04 1.18 [1.09-1.28] 0.09
17 ORMDL3/GSDML rs8079416 C/T 0.435 0.461 1.13E-03 0.90 [0.85-0.94] 0.01
1 - rs6679637 A/G 0.100 0.116 2.35E-03 0.85 [0.77-0.94] 0.03
1 CSFR3 rs4653210 G/T 0.111 0.122 3.71E-03 0.86 [0.78-0.95] 0.02
3 PPARG/ TSEN2 rs9855622 T/C 0.124 0.110 4.75E-03 1.14 [1.01-1.30] 2.94E-03
7 CACNA2D1 rs1544461 A/G 0.429 0.409 5.14E-03 1.09 [1.02-1.16] 7.81E-04
18 CNDP2 rs2241508 G/A 0.421 0.401 5.26E-03 1.09 [1.03-1.15] 2.94E-04
11 PHF21A/CREB3L1 rs7128538 A/G 0.491 0.470 5.51E-03 1.09 [1.02-1.16] 4.62E-03
14 NPAS3 rs1299512 G/A 0.228 0.211 7.76E-03 1.10 [1.00-1.21] 0.05
13 RFC3 rs7335534 G/A 0.398 0.415 8.61E-03 0.91 [0.84-0.99] 7.34E-04
8 DDEF1 rs7817803 A/C 0.437 0.421 0.012 1.08 [1.01-1.15] 2.01E-03
8 DDE/ rs3057 C/T 0.439 0.423 0.012 1.08 [1.01-1.15] 1.13E-03
17 TMEM132E/CCDC16 rs887081 T/G 0.115 0.129 0.013 0.88 [0.810.95] 5.33E-03
5 CDH18 rs1911856 T/C 0.059 0.048 0.013 1.18 [1.03-1.35] 3.24E-03
7 CAV1 rs2402091 A/G 0.110 0.122 0.014 0.88 [0.80-0.97] 0.02
7 - rs1228966 A/G 0.222 0.208 0.015 1.09 [1.01-1.18] 2.29E-03
7 SEMA3A rs1228870 T/G 0.222 0.208 0.017 1.09 [1.01-1.18] 3.15E-03
5 LOC389293 rs7708428 G/A 0.401 0.418 0.019 0.92 [0.87-0.98] 0.01
9 XPA rs2808699 A/C 0.403 0.423 0.021 0.92 [0.87-0.98] 2.38E-04
8 DDEF1 rs7839523 G/T 0.440 0.425 0.021 1.07 [1.011-1.14] 1.10E-03
9 XPA rs2805790 A/G 0.403 0.422 0.022 0.92 [0.87-0.98] 3.37E-04
3 IRAK2 rs11706450 T/C 0.465 0.482 0.024 0.93 [0.86-1.01] 9.00E-03
9 XPA rs2805815 A/G 0.403 0.422 0.024 0.93 [0.87-0.99] 3.02E-04
2 NOL10 rs4668690 A/G 0.067 0.059 0.026 1.15 [1.01-1.30 3.10E-03
7 - rs1029541 T/C 0.230 0.219 0.028 1.08 [1.01-1.17] 8.07E-04
9 XPA rs2668797 A/G 0.071 0.112 0.029 0.933 [0.87-0.99] 2.48E-04
14 - rs1036570 A/G 0.322 0.335 0.032 0.92 [0.85-1.014] 2.13E-03
3 - rs4128236 T/C 0.322 0.306 0.034 1.07 [0.98-1.17] 3.87E-04
1 - rs10925871 A/G 0.193 0.181 0.038 1.08 [1.00-1.17] 6.22E-03
7 CADPS2 rs2501439 G/A 0.418 0.432 0.042 0.93 [0.87-0.99] 7.49E-03
7 - rs757747 T/C 0.229 0.218 0.047 1.07 [1.00-1.16] 1.29E-03
7 WBSCR17 rs4585627 T/C 0.323 0.308 0.051 1.07 [1.00-1.14] 4.70E-03
10 - rs1254860 C/T 0.110 0.100 0.064 1.09 [0.99-1.21] 0.03
8 DDEF1 rs6470805 G/A 0.333 0.344 0.069 0.94 [0.88-1.00] 4.88E-03
9 LCN9 rs541131 G/A 0.400 0.385 0.071 1.06 [0.99-1.12] 1.78E-03
5 CDH18 rs2202798 T/C 0.080 0.069 0.078 1.11 [0.98-1.24] 9.17E-04
3 TDGF1 rs6799581 G/T 0.260 0.268 0.080 0.94 [0.86-1.03] 6.85E-04
5 CDH18 rs12655266 A/G 0.074 0.065 0.111 1.10 [0.98-1.24] 1.09E-03
4 NPY2R rs2880417 G/A 0.292 0.281 0.117 1.05 [0.99-1.13] 2.07E-05
7 - rs10272701 T/C 0.192 0.183 0.130 1.06 [0.98-1.15] 7.73E-03
8 FBX032 rs3739284 C/T 0.219 0.224 0.148 0.94 [0.87-1.01] 3.71E-03
6 ASCC3 rs7771570 C/T 0.492 0.482 0.153 1.04 [0.98-1.11] 2.97E-04
18 PHLPP rs2877745 T/C 0.091 0.084 0.158 1.08 [0.98-1.18] 3.49E-03
21 - rs2831511 T/C 0.393 0.403 0.175 0.95 [0.90-1.01] 1.54E-04
11 OPCML rs10894623 T/G 0.291 0.281 0.175 1.04 [0.95-1.14] 8.98E-04
6 ASCC3 rs6919745 T/C 0.476 0.467 0.190 1.042 [0.98-1.11] 1.88E-04
4 NPY2R rs13138293 G/T 0.308 0.299 0.195 1.05 [0.97-1.11] 8.20E-05
15 SMAD3 rs4147358 A/C 0.237 0.243 0.203 0.95 [0.86-1.04] 4.76E-04
17 TMEM132E rs4795032 T/C 0.351 0.341 0.232 1.04 [0.95-1.13] 6.65E-04
9 - rs10756265 A/G 0.342 0.352 0.251 0.96 [0.90-1.02] 2.18E-04
9 - rs443042 G/A 0.366 0.376 0.261 0.96 [0.90-1.02] 2.01E-04
9 SUSD3 rs9696357 T/C 0.154 0.160 0.268 0.95 [0.87-1.03] 2.11E-03
12 SFRS8 rs10794423 C/T 0.439 0.442 0.282 0.96 [0.89-1.04] 1.22E-03
2 ATP6V1C2 rs7422405 A/G 0.428 0.433 0.385 0.97 [0.91-1.03] 1.93E-04
3 RBMS3 rs35883 A/G 0.457 0.4564 0.556 1.019 [0.94-1.10] 1.04E-04
21 CHODL/ PRSS7 rs2248200 C/T 0.484 0.4815 0.598 1.01 [0.96-1.07] 1.35E-03
21 CHODL/PRSS7 rs1688165 A/G 0.485 0.4820 0.628 1.01 [0.96-1.07] 8.62E-04
16 ZNF423 rs1477020 T/C 0.121 0.1235 0.649 0.97 [0.86-1.10] 8.30E-06
1 C1QB rs631090 C/T 0.073 0.0702 0.729 1.02 [0.90-1.15] 3.73E-04
16 ZNF423 rs1990629 G/A 0.128 0.1308 0.736 0.98 [0.87-1.10] 2.13E-05
11 OPCML rs11223273 T/C 0.275 0.2721 0.759 1.01 [0.92-1.10] 1.40E-04
19 TSPAN16 rs322151 T/C 0.252 0.2527 0.990 0.99 [0.94-1.06] 3.37E-04
  1. N, 2,921 SSc/6,963 controls. aOdds ratio for the minor allele. Chr, chromosome; CI, confidence interval; MAF, minor allele frequency; OR, odds ratio; PBD, Breslow–Day test P value; PMH, allelic Mantel-Haenszel fixed effects model P value; SNP, single nucleotide polymorphism.