Table 1.

Single locus analysis of previous SLE associations outside of HLA region

Marker	ChrA	Position	Upstream Gene	Downstream Gene	Within Gene	MAFB	PGWAS	Model	Obs/ImpC	OR (95% CID)	Maj/MinE
rs1234314	1	173177392	1kb from TNFSF4	269kb from PRDX6	-	0.37	9.25×10−11	Add	Imp	1.37 (1.25-1.51)	C/G
rs2205960	1	173191475	15kb from TNFSF4	255kb from PRDX6	-	0.25	1.03×10−11	Add	Imp	1.44 (1.30-1.60)	G/T
rs76413021	1	173206297	30kb from TNFSF4	240kb from PRDX6	-	0.23	3.26×10−13	Add	Imp	1.52 (1.36-1.71)	G/A
rs844644	1	173209495	33kb from TNFSF4	237kb from PRDX6	-	0.4	4.47×10−11	Add	Obs	1.37 (1.25-1.50)	A/C
rs10489265	1	173236065	60kb from TNFSF4	211kb from PRDX6	-	0.25	8.19×10−12	Add	Obs	1.43 (1.29-1.58)	A/C
rs4916342	1	173347837	172kb from TNFSF4	99kb from PRDX6	-	0.3	8.22×10−9	Add	Imp	0.75 (0.67-0.82)	A/G
rs16833239	2	191940260	-	-	STAT4	0.15	9.69×10−10	Add	Imp	0.67 (0.59-0.76)	G/A
rs11889341	2	191943742	-	-	STAT4	0.32	8.02×10−19	Add	Obs	1.53 (1.40-1.69)	C/T
rs12612769	2	191953998	-	-	STAT4	0.31	2.37×10−19	Add	Imp	1.59 (1.43-1.75)	A/C
rs13192841	6	137967214	152kb from OLIG3	221kb from TNFAIP3	-	0.13	7.50×10−3	Dom	Obs	1.23 (1.06-1.43)	G/A
rs5029937	6	138195151	-	-	TNFAIP3	0.07	3.98×10−14	Dom	Imp	2.11 (1.74-2.55)	G/T
rs5029939	6	138195723	-	-	TNFAIP3	0.07	4.09×10−14	Dom	Imp	2.10 (1.74-2.55)	C/G
rs2230926	6	138196066	-	-	TNFAIP3	0.07	2.34×10−14	Dom	Obs	1.93 (1.63-2.28)	T/G
rs9373203	6	138289848	86kb from TNFAIP3	120kb from PERP	-	0.37	4.89×10−6	Add	Imp	1.25 (1.14-1.37)	C/T
rs6922466	6	138444930	16kb from PERP	38kb from KIAA1244	-	0.18	0.297	Dom	Obs	1.08 (0.94-1.24)	A/G
rs11185602	7	50299077	100kb from C7orf72	45kb from IKZF1	-	0.33	1.53×10−16	Add	Imp	0.66 (0.60-0.73)	A/G
rs17552904	7	50318308	120kb from C7of72	26kb from IKZF1	-	0.33	3.51×10−16	Add	Obs	0.65 (0.59-0.72)	G/T
rs6964720	7	75180344	-	-	HIP1	0.24	2.00×10−10	Add	Obs	1.40 (1.26-1.56)	A/G
rs139110493	7	75209951	-	-	HIP1	0.06	1.21×10−12	Dom	Imp	2.48 (1.93-3.19)	G/C
rs4728142	7	128573967	11kb from LOC392787	4kb from IRF5	-	0.14	1.38×10−11	Add	Obs	1.53 (1.35-1.73)	G/A
rs113478424	7	128575797	13kb from LOC392787	2kb from IRF5	-	0.14	3.97×10−12	Add	Imp	1.59 (1.39-1.81)	15-mer*/T
rs922483	8	11351912	-	-	BLK	0.25	2.00×10−10	Add	Obs	0.71 (0.64-0.79)	T/C
rs2736345	8	11352485	-	-	BLK	0.24	7.88×10−11	Add	Imp	0.70 (0.63-0.78)	G/A
rs10857631	10	49955821	-	-	WDFY4	0.13	1.67×10−4	Add	Imp	1.30 (1.13-1.48)	A/G
rs7097397	10	50025396	-	-	WDFY4	0.37	2.10×10−9	Add	Obs	1.33 (1.21-1.46)	A/G
rs877819	10	50042951	-	-	WDFY4	0.16	0.0558	Add	Imp	1.13 (1.00-1.28)	G/A
rs10776651	10	50084526	-	-	WDFY4	0.34	1.54×10−7	Add	Imp	1.29 (1.18-1.43)	C/T
rs1913517	10	50119054	-	-	WDFY4	0.31	2.54×10−5	Add	Obs	1.24 (1.12-1.37)	G/A
rs12576753	11	128304141	None within 500kb	25kb from ETS1	-	0.39	1.74×10−11	Add	Obs	1.37 (1.25-1.56)	C/A
rs1128334	11	128328959	-	-	ETS1	0.38	7.17×10−12	Add	Imp	1.39 (1.26-1.52)	G/A
rs5986948	X	153266172	17.3kb from TMEM187	9.8kb from IRAK1	-	0.24	4.36 ×10−10	Rec	Imp	0.64 (0.56-0.74)	C/T
rs1059702	X	153284192	-	-	IRAK1	0.26	5.14×10−10	Rec	Imp	0.65 (0.57-0.74)	A/G
rs2734647	X	153292180	-	-	MECP2	0.25	7.54×10−9	Dom	Obs	0.62 (0.51-0.75)	T/C

^AChr = Chromosome

^BMAF = Minor allele frequency

^CObs/Imp = observed/imputed

^DCI = Confidence interval

^EMaj/Min = Major/Minor allele

^*15-mer= CTTAGCTATTGCTC