Table 1.

Differentially methylated CpGs and assigned genes in different comparisons. Statistical analysis was performed using the logit transformed M-values for methylation. Differentially methylated CpGs were assigned using Limma (version 3.36.1) and adjusted for status, gender and ethnicity as confounders. A 5% Benjamini-Hochberg False Discovery Rate (FDR) correction for multiple testing was applied. All dmCpGs were assigned to their corresponding genomic context and location using the R/Bioconductor package IlluminaHumaMethylationEPICanno.ilm10b2.hg19 (version 0.6.0). ICP: intrahepatic cholestasis of pregnancy; logFC: log fold change; UCSC: University of California, Santa Cruz genome browser.

Comparison	CpG site	Status	logFC	P.Value	Adjusted P value	Symbol	UCSC Reference Gene Name
Control versus disease (treated and untreated ICP)	cg13274534	Hypermethylated in disease	−0.243564	4.64E-08	0.02264796	TEX29	testis expressed 29
	cg00720629	Hypermethylated in disease	−0.3728101	1.89E-07	0.02264796	TBX1	T- box 1
	cg09781936	Hypermethylated in disease	−0.2377453	2.72E-07	0.02264796	TBX1	T-box 1
	cg18351741	Hypermethylated in disease	−0.3198715	3.09E-07	0.02264796	DFNB59	deafness, autosomal recessive 59
	cg10034679	Hypermethylated in disease	−0.247224	3.19E-07	0.02264796	WDFY4	WDFY family member 4
	cg01520190	Hypermethylated in disease	−0.2302545	3.80E-07	0.02264796	AHNAK	AHNAK nucleoprotein
	cg17676618	Hypermethylated in disease	−0.2464	4.90E-07	0.02544932
	cg16850951	Hypermethylated in disease	−0.3245504	8.75E-07	0.03848915
	cg03354554	Hypomethylated in disease	0.47555505	1.79E-07	0.02264796
	cg23530232	Hypomethylated in disease	0.40697096	2.52E-07	0.02264796	H6PD	hexose-6-phosphate dehydrogenase/ glucose 1-dehydrogenase
	cg08282819	Hypomethylated in disease	0.40336227	2.59E-07	0.02264796	IL21R	interleukin 21 receptor
	cg05018116	Hypomethylated in disease	0.33289686	2.90E-07	0.02264796	BRD4	bromodomain containing 4
	cg10961050	Hypomethylated in disease	0.33797259	3.01E-07	0.02264796	MAMDC2	MAM domain containing 2
	cg25975961	Hypomethylated in disease	0.52015521	3.37E-07	0.02264796
	cg22559497	Hypomethylated in disease	0.43934031	3.75E-07	0.02264796
	cg20334115	Hypomethylated in disease	0.50811853	4.00E-07	0.02264796	PYCR2	pyrroline-5-carboxylate reductase 2
	cg25001190	Hypomethylated in disease	0.33147151	5.14E-07	0.02544932	NFIA	nuclear factor I A
	cg06313424	Hypomethylated in disease	0.31707252	6.02E-07	0.02803589	WDR70	WD repeat domain 70
Control versus untreated ICP	cg03749207	Hypomethylated in untreated ICP	1.742272	5.82E-09	0.00460946	PRR25	proline rich 25
	cg02407415	Hypomethylated in untreated ICP	1.449036	5.37E-08	0.02125066	PRR25	proline rich 25
Treated versus untreated ICP	cg03749207	Hypomethylated in untreated ICP	1.789117	2.18E-10	0.00017294	PRR25	proline rich 25
	cg02407415	Hypomethylated in untreated ICP	1.425257	8.48E-09	0.00335754	PRR25	proline rich 25