Table 3.

Top differentially methylated CpG sites (DMCs) in the case-case analysis between patients with systemic lupus erythematosus (SLE) and patients with primary Sjögren's syndrome (pSS).

CpG site	Position (chr:bp)	Gene	Gene name	Mean meth-β in SLE	Mean meth-β in pSS	Δβ SLE-pSS§	p-value SLE-pSS‡
cg21549285	21:42799141	MX1	MX dynamin like GTPase 1	0.41	0.57	−0.16	1.1 × 10−08
cg05552874	10:91153143	IFIT1	Interferon induced protein with tetratricopeptide repeats 1	0.46	0.57	−0.11	8.1 × 10−11
cg03546163	6:35654363	FKBP5	FKBP prolyl isomerase 5	0.47	0.58	−0.10	1.8 × 10−16
cg04858164	15:57324333	TCF12	Transcription factor 12	0.46	0.56	−0.10	2.9 × 10−31
cg09166556	1:156724277	NA		0.55	0.65	−0.10	1.3 × 10−40
cg09010699	3:195171693	NA		0.43	0.53	−0.10	1.3 × 10−68
cg13984928	17:3704574	ITGAE	Integrin subunit alpha E	0.38	0.48	−0.09	2.0 × 10−33
cg21201401	20:62367884	LIME1	Lck interacting transmembrane adaptor 1	0.56	0.47	0.09	6.5 × 10−23
cg16672562	19:46801672	HIF3A	Hypoxia inducible factor 3 subunit alpha	0.36	0.45	−0.09	2.3 × 10−11
cg19055828	12:51139321	DIP2B	Disco interacting protein 2 homolog B	0.40	0.49	−0.09	1.3 × 10−55
cg15086439	1:236563070	EDARADD	EDAR associated death domain	0.38	0.47	−0.09	1.9 × 10−34
cg20934416	5:17444401	NA		0.43	0.52	−0.09	4.3 × 10−34
cg01079652	1:79118191	IFI44	Interferon induced protein 44	0.71	0.80	−0.09	2.0 × 10−09
cg20700740	1:9339683	NA		0.36	0.45	−0.09	1.6 × 10−42
cg19460836	17:79047872	BAIAP2	BAI1 associated protein 2	0.44	0.53	−0.09	2.4 × 10−40
cg00446123	20:62367888	LIME1	Lck interacting transmembrane adaptor 1	0.66	0.56	0.09	8.1 × 10−38
cg10408731	7:65214843	LOC441242		0.42	0.51	−0.09	5.3 × 10−36
cg07110356	17:56355431	MPO	Myeloperoxidase	0.42	0.51	−0.09	4.1 × 10−40
cg00980622	14:75884845	NA		0.41	0.50	−0.09	2.9 × 10−43
cg26298914	14:68798365	RAD51B	RAD51 paralog B	0.38	0.47	−0.09	5.9 × 10−49
cg13381110	18:60646614	PHLPP1	PH domain and leucine rich repeat protein phosphatase 1	0.53	0.62	−0.09	2.8 × 10−20
cg03637218	5:115209107	AP3S1	Adaptor related protein complex 3 subunit sigma 1	0.44	0.53	−0.09	3.9 × 10−37
cg16125725	15:70101302	NA		0.41	0.50	−0.09	9.7 × 10−39
cg25757820	2:224819307	NA		0.46	0.55	−0.09	4.7 × 10−53
cg25600606	11:33308345	HIPK3	Homeodomain interacting protein kinase 3	0.48	0.57	−0.09	1.0 × 10−51
cg10665891	12:117042917	NA		0.38	0.48	−0.09	2.8 × 10−32
cg25344401	7:4755415	FOXK1	Forkhead box K1	0.44	0.53	−0.09	7.0 × 10−34
cg03340036	4:89446409	PIGY	Phosphatidylinositol glycan anchor biosynthesis class Y	0.45	0.54	−0.09	1.5 × 10−37
cg13618969	9:129184186	MVB12B	Multivesicular body subunit 12B (FAM125B)	0.49	0.58	−0.09	8.1 × 10−39
cg23338668	8:74240259	NA		0.47	0.56	−0.09	1.3 × 10−37

The 30 DMCs with the largest absolute difference in mean methylation (|Δβ|) comparing SLE and pSS are listed.

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

^‡P-value of the case-case association analysis of differential DNA methylation between SLE and pSS.

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