Table 1

Top differentially methylated CpG sites (DMCs) in the systemic lupus erythematosus case–control association analysis

Chromosome	Position	CpG site	Gene	Interferon induced*	Discovery		Replication
Chromosome	Position	CpG site	Gene	Interferon induced*	P value†	Methylation Δβ‡	P value†	Methylation Δβ‡
21	42799141	cg21549285	MX1	Yes	3.5E−139	−0.42	6.4E− 83	−0.47
3	122281881	cg22930808	PARP9	Yes	1.4E−105	−0.27	1.2E−74	−0.33
21	42797588	cg22862003	MX1	Yes	2.5E−126	−0.27	1.8E−77	−0.30
1	79088769	cg05696877	IFI44L	Yes	1.9E−120	−0.26	4.1E−86	−0.32
1	79085586	cg03607951	IFI44L	Yes	3.0E−141	−0.25	4.8E−83	−0.27
10	91153143	cg05552874	IFIT1	Yes	2.5E−128	−0.25	1.8E−73	−0.27
3	146260954	cg06981309	PLSCR1	Yes	4.9E− 157	−0.24	7.6E−91	−0.25
3	122281975	cg00959259	PARP9	Yes	9.3E−105	−0.23	6.1E−71	−0.27
11	315102	cg23570810	IFITM1	Yes	1.6E−5	−0.20	3.4E−60	−0.24
21	42797847	cg26312951	MX1	Yes	1.3E−82	−0.18	1.2E−59	−0.22
22	50971140	cg20098015	ODF3B	Yes	7.1E−96	−0.15	1.1E−52	−0.16
2	7004578	cg01028142	CMPK2	Yes	1.2E−64	−0.15	4.5E−47	−0.19
1	79085713	cg17980508	IFI44L	Yes	3.8E−179	−0.14	1.1E−79	−0.13
8	66751182	cg14864167	PDE7A	Yes	3.6E−41	−0.14	4.0E−37	−0.20
8	144099482	cg17052170	LOC100133669,LY6E	Yes	1.5E−58	−0.13	2.6E−35	−0.15
11	319667	cg09122035	Intergenic	NA	3.1E−72	−0.13	9.9E−41	−0.13
11	319555	cg20045320	Intergenic	NA	1.0E−63	−0.13	8.3E−38	−0.13
11	614761	cg08926253	IRF7	Yes	6.8E−81	−0.13	1.5E−54	−0.14
1	79085162	cg13304609	IFI44L	Yes	5.0E−63	−0.13	3.3E−47	−0.16
6	35654363	cg03546163	FKBP5	Yes	1.5E−66	−0.13	1.8E−24	−0.11
22	50973101	cg05523603	Intergenic	NA	4.7E−71	−0.13	2.0E−50	−0.14
16	87371097	cg01787084	FBXO31	NA	1.4E−126	−0.13	8.3E−61	−0.10
11	315262	cg03038262	IFITM1	Yes	1.6E−50	−0.12	2.7E−48	−0.17
1	79118191	cg01079652	IFI44	Yes	3.6E−43	−0.12	1.7E−25	−0.13
7	2444534	cg10152449	CHST12	Yes	3.6E−102	−0.11	3.5E−49	−0.10
6	29911550	cg17608381	HLA-A	Yes	4.8E−25	−0.11	4.1E−15	−0.12
2	7018020	cg10959651	RSAD2	Yes	2.9E−110	−0.11	3.1E−66	−0.12
11	319718	cg17990365	IFITM3	Yes	9.5E−56	−0.11	1.5E−35	−0.11
1	79085765	cg00855901	IFI44L	Yes	1.0E−135	−0.11	2.6E−70	−0.11
2	7016509	cg23213327	RSAD2	Yes	4.7E−92	−0.10	8.0E−58	−0.10
20	62204908	cg01190666	PRIC285 (HELZ2)	Yes	1.2E−111	−0.10	5.7E−61	−0.11
3	45984838	cg08450017	CXCR6,FYCO1 (RUFY3)	Yes	1.4E− 130	0.13	1.8E−51	0.10

DMCs with |Δβ| > 0.1 in both the discovery and replication cohorts are listed.
*Database of interferon-regulated genes http://interferome.org.
†P value for case–control comparison using a linear regression model containing cell count estimates, age and sex as covariates.
‡Difference in average methylation beta value between patients and control individuals.