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Table 2 Analysis of rs310746 and rs6832151 minor allele frequencies in the GWASs, replication, and combined cohorts

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

Cohort, N(cases/controls) Chr Locus SNP Minor/major MAF cases MAF controls P MH OR (CI 95%)a P BD
GWASs 3 SYN2|PPARG rs310746 C/T 0.108 0.087 1.90E-06 1.28 [1.12-1.47] 0.334
2921/6963 4 CHRNA9|RHOH rs6832151 G/T 0.315 0.282 4.30E-06 1.17 [1.075-1.27] 0.054
Replication 3 SYN2|PPARG rs310746 C/T 0.099 0.103 0.066 1.17 [0.99-1.38] 0.231
1068/6762 4 CHRNA9|RHOH rs6832151 G/T 0.296 0.280 0.962 0.99 [0.89-1.11] 0.934
Combined 3 SYN2|PPARG rs310746 C/T 0.106 0.094 5.00E-07 1.25 [1.15-1.37] 0.324
3989/13725 4 CHRNA9|RHOH rs6832151 G/T 0.310 0.281 1.07E-04b 1.12 [1.06-1.19] 0.017
  1. aOdds ratio for the minor allele. bP value from meta-analysis under random effects = 0.051; OR = 1.10 (0.99-1.22).
  2. 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.