Table 1.

Characteristics of disease associated variants at sixteen SLE risk loci.

DOI: http://dx.doi.org/10.7554/eLife.12089.006

Risk locus	Signal	Peak SNP	Minor allele	Odds ratio (Minor allele)	Allele Freq. (Cases)	Allele Freq. (Controls)	SLE association P-value	SLE associated Annotated variants	Variants in LD with peak SNP (D' >0.8)
									Total variants	Total potentially functional variants	Total coding variants
STAT4	1	rs12612769	C	1.7	0.29	0.19	5E-10	52	49	9	0
HLA-D	1	rs9271593 (XL9)	C	1.7	0.55	0.42	7E-10	835	530	398	0
	2	rs9274678 (DQB1)	G	2.1	0.24	0.13	6E-09	736	216	69	0
	3	rs36101847 (DRB1)	T	0.5	0.13	0.23	8E-09	760	296	126	0
ITGAM-ITGAX	1	rs41476751	C	1.9	0.25	0.15	8E-09	153	121	62	3
IRF5_TNPO3	1	rs34350562	G	1.8	0.23	0.14	3E-09	245	189	124	0
UBE2L3	1	rs181366	T	1.5	0.27	0.20	2E-07	82	79	55	1
BANK1	1	rs4699260	T	0.7	0.20	0.28	9E-06	267	143	29	2
TNIP1	1	rs62382335	A	1.4	0.14	0.10	6E-05	46	22	16	0
TNFAIP3	1	rs57087937	T	1.9	0.10	0.06	2E-06	69	63	40	1
CCL22-CX3CL1	1	rs223889	T	1.5	0.34	0.27	5E-07	32	25	20	0
RAVER1-ZGLP1	1	rs35186095	T	1.3	0.21	0.17	2E-04	43	24	19	0
ICA1	1	rs74787882	A	0.7	0.06	0.09	2E-03	34	10	6	0
TNFSF4	1	rs1819717	G	0.7	0.29	0.36	2E-05	73	30	14	0
	2	rs4916313	C	1.3	0.39	0.32	2E-04		30	21	0
BLK	1	rs7822109	C	0.8	0.46	0.52	9E-05	97	61	38	0
XKR6	1	rs4840545	A	2.0	0.13	0.07	1E-07	335	51	23	0
	2	rs7000132	C	0.9	0.42	0.46	5E-04		178	118	0
NMNAT2-SMG7	1	rs41272536	G	2.9	0.11	0.05	2E-08	33	8	8	0
	2	rs111487113	A	0.6	0.13	0.18	5E-04		17	5	0
ETS1	1	rs34516251	A	0.8	0.18	0.21	7E-03	18	10	6	0