Table 1. Novel non-HLA loci associated with SSc clinical and serological subtypes.

SSc Subphenotype	Chr.	Gene	SNP	Base Pair	Location	Change	Stage	N (case/control)	MAF (case/control)	P † value	OR (95% CI)
lcSSc	7p12.1	GRB10	rs12540874	50,632,416	Intronic	G/A	GWAS	1400/5172	0.461/0.409	3.00×10−6	1.23 (1.13-1.34)
							Replication	1960/4971	0.416/0.395	3.07×10−2	1.09 (1.01–1.18)
							Combined	3360/10143	0.435/0.403	1.27×10−6	1.15 (1.09–1.22)
	16q24.1	IRF8	rs11642873	84,549,206	Intergenic	C/A	GWAS	1400/5172	0.144/0.197	1.39×10−7	0.72 (0.64–0.81)
							Replication	1960/4971	0.143/0.186	6.88×10−6	0.78 (0.70–0.87)
							Combined	3360/10143	0.144/0.192	2.32×10−12	0.75 (0.69–0.81)
dcSSc	12q13.2	RPL41/ESYT1 *	rs11171747	54,804,675	Upstream	G/T	GWAS	740/5172	0.446/0.384	2.19×10−6	1.31 (1.01–1.29)
							Replication	959/4971	0.408/0.372	3.49×10−3	1.16 (1.15–1.71)
							Combined	1699/10143	0.425/0.379	5.99×10−8	1.23 (1.10–1.50)
ACA+	12p12.1	SOX5	rs11047102	23,837,413	Intronic	T/C	GWAS	761/5172	0.132/0.096	1.03×10−5	1.47 (1.24–1.73)
							Replication	1030/4971	0.123/0.102	2.91×10−3	1.27 (1.09–1.48)
							Combined	1791/10143	0.127/0.099	1.39×10−7	1.36 (1.21–1.52)

†: P values for GWAS cohorts are Mantel-Haenszel meta-analysis GC corrected according to the set λ and in the replication and combined analysis Mantel-Haenszel meta-analysis P value.

*Association in rs11171747 had a significant BD P value, thus making it heterogeneous association among populations.