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

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

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-04^b	1.12 [1.06-1.19]	0.017

^aOdds ratio for the minor allele. ^bP value from meta-analysis under random effects = 0.051; OR = 1.10 (0.99-1.22).
Chr, chromosome; CI, confidence interval; MAF, minor allele frequency; OR, odds ratio; P_BD, Breslow–Day test P value; P_MH, allelic Mantel-Haenszel fixed-effects model P value; SNP, single-nucleotide polymorphism.

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