Table 1.

Top shared differentially methylated sites (DMCs) between the SLE case-control EWAS and the pSS case-control EWAS.

CpG site	Position (chr:bp)	Gene	Gene name	Mean meth-β in SLE	Mean meth-β in pSS	Mean meth-β in ctrl	Δβ SLE- ctrl§	Δβ pSS- ctrl§	p-value EWAS SLE-ctrl‡	p-value EWAS pSS- ctrl‡
cg03607951	1:79085586	IFI44L	Interferon induced protein 44 like	0.34	0.41	0.59	−0.25	−0.18	3.0 × 10−141	9.9 × 10−67
cg05696877	1:79088769	IFI44L	Interferon induced protein 44 like	0.41	0.47	0.67	−0.26	−0.20	1.9 × 10−120	2.9 × 10−50
cg01028142	2:7004578	CMPK2	Cytidine/uridine monophosphate kinase 2	0.73	0.81	0.88	−0.15	−0.07	1.2 × 10−64	2.8 × 10−32
cg10959651	2:7018020	RSAD2	Radical S-adenosyl methionine domain containing 2	0.16	0.19	0.27	−0.11	−0.07	2.9 × 10−110	1.3 × 10−34
cg22930808	3:122281881	PARP9	Poly(ADP-ribose) polymerase family member	0.43	0.52	0.71	−0.27	−0.19	1.4 × 10−105	2.4 × 10−55
cg00959259	3:122281975	PARP9	Poly(ADP-ribose) polymerase family member	0.35	0.41	0.58	−0.23	−0.17	9.3 × 10−105	2.6 × 10−48
cg06981309	3:146260954	PLSCR1	Phospholipid scramblase 1	0.30	0.39	0.54	−0.24	−0.15	4.9 × 10−157	4.1 × 10−51
cg17608381	6:29911550	HLA-A	Major histocompatibility complex, class I, A	0.49	0.48	0.60	−0.11	−0.12	4.8 × 10−25	3.4 × 10−15
cg07180897	6:32729130	HLA-DQB2	Major histocompatibility complex, class II, DQ beta 2	0.74	0.73	0.81	−0.07	−0.08	2.7 × 10−10	8.9 × 10−07
cg10152449	7:2444534	CHST12	Carbohydrate sulfotransferase 12	0.27	0.31	0.39	−0.11	−0.08	3.6 × 10−102	9.5 × 10−28
cg14864167	8:66751182	PDE7A	Phosphodiesterase 7A	0.51	0.57	0.65	−0.14	−0.08	3.6 × 10−41	1.3 × 10−18
cg11317199	9:100850391	TRIM14	Tripartite motif containing 14	0.68	0.66	0.59	0.09	0.07	1.5 × 10−33	1.1 × 10−15
cg05552874	10:91153143	IFIT1	Interferon induced protein with tetratricopeptide repeats 1	0.46	0.57	0.71	−0.25	−0.14	2.5 × 10−128	2.7 × 10−56
cg01971407	11:313624	IFITM1	Interferon induced transmembrane protein 1	0.40	0.41	0.48	−0.08	−0.07	3.8 × 10−53	3.3 × 10−30
cg23570810	11:315102	IFITM1	Interferon induced transmembrane protein 1	0.49	0.55	0.69	−0.20	−0.14	1.6 × 10−75	6.1 × 10−38
cg03038262	11:315262	IFITM1	Interferon induced transmembrane protein 1	0.45	0.48	0.57	−0.12	−0.09	1.6 × 10−50	2.7 × 10−32
cg20045320	11:319555	NA		0.43	0.46	0.55	−0.13	−0.10	1.0 × 10−63	5.3 × 10−26
cg09122035	11:319667	NA		0.36	0.40	0.49	−0.13	−0.09	3.1 × 10−72	1.5 × 10−20
cg17990365	11:319718	IFITM3	Interferon induced transmembrane protein 3	0.50	0.53	0.61	−0.11	−0.08	9.5 × 10−56	5.9 × 10−23
cg08926253	11:614761	IRF7	Interferon regulatory factor 7	0.47	0.52	0.60	−0.13	−0.08	6.8 × 10−81	3.8 × 10−34
cg27209729	11:64428925	NRXN2	Neurexin 2	0.54	0.53	0.61	−0.08	−0.08	9.3 × 10−50	4.6 × 10−27
cg03172657	16:89163625	ACSF3	Acyl-CoA synthetase family member 3	0.53	0.53	0.45	0.08	0.07	4.6 × 10−34	3.8 × 10−13
cg10604476	19:10403908	ICAM5	Intercellular adhesion molecule 5	0.55	0.57	0.48	0.07	0.09	1.1 × 10−13	5.8 × 10−11
cg05825244	20:2730488	EBF4	EBF family member 4	0.54	0.57	0.47	0.07	0.11	2.3 × 10−11	2.4 × 10−11
cg22862003	21:42797588	MX1	MX dynamin like GTPase 1	0.43	0.51	0.70	−0.27	−0.19	2.5 × 10−126	7.9 × 10−63
cg26312951	21:42797847	MX1	MX dynamin like GTPase 1	0.26	0.29	0.44	−0.18	−0.14	1.3 × 10−82	1.3 × 10−41
cg21549285	21:42799141	MX1	MX dynamin like GTPase 1	0.41	0.57	0.83	−0.42	−0.26	3.5 × 10−139	6.9 × 10−59
cg20098015	22:50971140	ODF3B	Outer dense fiber of sperm tails 3B	0.33	0.39	0.49	−0.15	−0.10	7.1 × 10−96	2.1 × 10−33
cg05523603	22:50973101	NA		0.59	0.64	0.72	−0.13	−0.08	4.7 × 10−71	3.8 × 10−26

DMCs with methylation |Δβ| > 0.07 in both case-control EWASs are listed ordered by their chromosomal position.

^§Methylation Δβ refers to the difference in mean methylation β between patients with SLE, respectively, pSS and control individuals, with a negative value representing decreased methylation in the patients.

^‡P-value for the case-control EWAS.

EWAS, epigenome-wide association study; meth-β, methylation β; NA, not annotated.