Table 3.

Candidate autoimmune loci with evidence of association to SLE

SNP	Gene	Chr	P				Combined corrected	Risk allele	Risk allele frequency	OR	Phenotype	References
			GWAS	US	Sweden	Combined
rs1990760	IFIH1	2	3.2 × 10−5	0.015	0.0039	3.34 × 10−7	1.12 × 10−5	T	0.60	1.17	T1D, Graves’	27,28
rs641153a	CFB	6	0.0079	n.a.	0.0011	1.4 × 10−4	0.0049	G	0.91	1.30	AMD	29
rs12708716a	CLEC16A	16	0.15	1.3 × 10−4	0.062	1.6 × 10−4	0.0056	A	0.64	1.16	T1D, Addison’s, MS	32–34
rs6887695a	IL12B	5	0.014	0.04	0.03	1.7 × 10−4	0.0060	G	0.68	1.13	Psoriasis, IBD	12,35
rs17696736	SH2B3	12	0.0036	0.12	0.19	4.0 × 10−4	0.014	T	0.50	1.08	T1D, Celiac, SLE	33,36,37

All alleles in the table either were identical to the reported variants or have r² > 0.8 to the reported variant and were the same risk allele with the same direction of effect. Samples, individual and combined P values, risk allele frequency and OR are as described in Table 1 legend. Combined-corrected P value is the Bonferroni-corrected P value for the 35 previously reported risk loci. Other autoimmunity associations: T1D, type 1 diabetes; AMD, age-related macular degeneration; MS, multiple sclerosis; IBD, inflammatory bowel disease. See Supplementary Table 3 for expanded summary statistics and a complete list of variants tested.

^aIndicates markers that were imputed, as described in Online Methods, from the GWAS samples and directly genotyped in the replication samples.