Table 2.

Differentially methylated CpG sites (DMCs) uniquely associated with primary Sjögren's syndrome (pSS)^*.

CpG site	Position (chr:bp)	Gene	p-value EWAS pSS-ctrl§	Δβ pSS-ctrl#	p-value EWAS SLE-ctrl†	Δβ SLE-ctrl#	Enhancer‡	Promoter¶	DHS**
cg21400344	1:25870172	LDLRAP1	2.7 × 10−12	−0.06	0.13	−0.0079	No	Yesa, b	Yesa, b
cg25824217	6:33040535	HLA-DPA1	1.0 × 10−11	−0.05	0.48	−0.0036	Yesa, b	Yesb	Yesa, b
cg12899747	3:25391527	NA	1.6 × 10−11	−0.06	0.21	−0.0076	No	No	No
cg08468401	3:14303131	NA	1.2 × 10−9	−0.05	0.85	−0.0011	No	No	Yesb
cg22805491	14:51172404	NA	1.0 × 10−7	0.08	0.10	0.0158	No	No	No

^*DMCs with p < 1.3 × 10⁻⁷ and average methylation difference |Δβ| > 0.05 in the pSS case-control EWAS, while p > 0.05 in the SLE case-control EWAS.

^§pSS case-control EWAS p-value.

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

^†SLE case-control EWAS p-value.

^‡Genomic location of DMC overlapping H3K27ac (active enhancer mark) peak in a) reference CD3⁺ T cells, and/or b) reference CD19⁺ B cells.

^¶Genomic location of DMC overlapping H3K4me3 (active promoter mark) peak in a) reference CD3⁺ T cells, and/or b) reference CD19⁺ B cells.

^**Genomic location of DMC overlapping DHS (indicating euchromatin) in a) reference CD3 ⁺ T cells, and/or ^b) reference CD19⁺ B cells.

DHS, DNase hypersensitivity site; EWAS, epigenome-wide association study; HLA-DPA1, major histocompatibility complex, class II, DP alpha 1; LDLRAP1, low density lipoprotein receptor adaptor protein 1; NA, not annotated.