Table 4.

Analysis of candidate genes from previous studies of SLE and other autoimmune disorders

Gene	Phenotype	Chr	Published SNP	Minor allele	MAF (affected women)	MAF (controls)	GWA P value	OR	95% CI
IL23R	CD	1p31.3	rs11209026	T	0.0671	0.0665	0.93	1.01	0.72–1.41
PTPN22	SLE, RA, T1D, AITD	1p13	rs2476601	A	0.1271	0.0862	5.2 × 10−6	1.53	1.27–1.84
FCGR2A	SLE	1q23	rs1801274	T	0.4319	0.5067	6.78 × 10−7	0.74	0.65–0.83
IFIH1	T1D	2q24	rs1990760	C	0.3706	0.4067	0.01	0.86	0.76–0.97
			rs3788964	G	0.1411	0.1544	0.22	0.90	0.76–1.07
STAT4	RA, SLE	2q32	rs7574865	T	0.3159	0.2346	2.8 × 10−9	1.50	1.24–1.82
			rs7601754	C	0.1340	0.1871	3.7 × 10−6	0.67	0.57–0.80
CAPSL	T1D	5p13	rs1445898	T	0.4451	0.4418	0.83	0.96	0.81–1.14
IL7R	MS, T1D	5p13	rs6897932	A	0.2556	0.2488	0.6	1.04	0.90–1.19
			rs1494558	T	0.3340	0.3387	0.74	0.98	0.82–1.17
			rs1494555	C	0.3299	0.3330	0.83	0.99	0.83–1.18
			rs3194051	C	0.2479	0.2738	0.05	0.88	0.76–1.00
SLC22A4	RA	5q31	rs2073838	A	0.0801	0.0773	0.73	1.04	0.76–1.41
TRAF1-C5	RA	9q33	rs7035682	A	0.0830	0.0841	0.89	0.99	0.73–1.34
			rs10985112	A	0.0751	0.0748	0.97	1.00	0.73–1.38
			rs7026551	G	0.1957	0.1737	0.002	1.90	1.25–2.88
			rs2269066	A	0.1035	0.0887	0.09	1.19	0.97–1.45
IL2RA	T1D, MS	10p15	rs7090530	G	0.4366	0.4124	0.10	1.10	0.98–1.25
			rs12251307	A	0.1292	0.1239	0.6	1.05	0.88–1.25
			rs7072793	C	0.3806	0.4165	0.01	0.86	0.76–0.97
			rs4147359	T	0.3090	0.3403	0.03	0.87	0.77–0.99
SH2B3	T1D	12q24	rs3184504	C	0.4588	0.4922	0.03	0.88	0.78–0.99
PTPN2	T1D	18p11	rs1893217	C	0.1625	0.1577	0.66	1.04	0.83–1.30
			rs478582	G	0.4638	0.4390	0.1	1.10	0.98–1.24
TYK2	SLE	19p13	rs280500	C	0.1557	0.1572	0.9	0.99	0.78–1.24
			rs6511696	A	0.0817	0.0788	0.72	1.03	0.76–1.40
			rs280519	A	0.5258	0.4915	0.03	1.14	1.01–1.28
			rs12720356	G	0.0744	0.0881	0.1	0.83	0.66–1.04

Shown here are results from our GWA data from the joint analysis of Sets 1 and 2 for previously described autoimmune-associated SNP_s. We also observed significant associations with rs12580100 (P = 0.0009), which is 35 kb from ERBB3 (T1D) and rs10800309 (P = 0.0007), which is 3.3 kb upstream from FCGR2A (SLE). Genes not evaluated include FCGR3A (SLE), PDCD1 (SLE), CARD15 (CD), CTLA4/ICOS (SLE, T1D), CRP (SLE) and FCRL3 (RA, SLE). The additive model is presented except for rs7026551 where the lack of fit to an additive model was significant (P < 0.05) and a recessive model is preferred. Abbreviations for phenotypes are as follows: AITD, autoimmune thyroid disease; CD, Crohn’s disease; MS, multiple sclerosis; RA, rheumatoid arthritis; SLE, systemic lupus erythematosus; T1D, type 1 diabetes. Other abbreviations are as listed in Table 1.