An Immunochip-based interrogation of scleroderma susceptibility variants identifies a novel association at DNASE1L3

Table 2 Association finding for previously reported loci achieving P <0.01 in Immunochip, with findings in replication and overall datasets

SNP	Chr	Location (hg18; bp)	Locus	MAF cases	MAF controls	OR	UnadjustedPvalue	Replication OR	ReplicationPvalue	Combined analysis	References
rs2056626	1	165,687,049	CD247	0.359	0.428	0.76	1.1 × 10⁻⁴	0.84	0.007	3.9 × 10⁻⁶	[6],[7],[11]
rs3821236	2	191,611,003	STAT4	0.255	0.194	1.41	2.6 × 10⁻⁵	1.24	0.008	1.2 × 10⁻⁶	[6],[7]
rs10168266	2	191,644,049	STAT4	0.249	0.190	1.40	4.1 × 10⁻⁵	1.30	0.001	1.9 × 10⁻⁷	[11]
rs7574865	2	191,672,878	STAT4	0.286	0.225	1.35	1.2 × 10⁻⁴	1.15	0.066	5.7 × 10⁻⁵	[7]
rs2176082	3	58,306,226	PXK	0.343	0.296	1.31	2.6 × 10⁻⁴	1.15	0.046	7.2 × 10⁻⁵	[16]
rs4728142	7	128,361,203	TNP03-IRF5	0.497	0.449	1.23	3.2 × 10⁻³	1.23	0.002	2.1 × 10⁻⁵	[6],[11]
rs10488631	7	128,381,419	TNP03-IRF5	0.156	0.114	1.50	2.4 × 10⁻⁵	1.36	0.001	1.6 × 10⁻⁷	[6],[7],[11]
rs12531711	7	128,404,702	TNP03-IRF5	0.156	0.113	1.51	2.1 × 10⁻⁵	1.38	0.001	8.6 × 10⁻⁸	[11]
rs1378942	15	72,864,420	CSK	0.379	0.319	1.27	8.7 × 10⁻⁴	1.17	0.023	7.8 × 10⁻⁵	[11]

ISSN: 1478-6362