TABLE 2.

DNA Methylation state of Crohn’s disease-related genes. NS, Non-surgical patients; S, surgical patients.

Gene symbol	Group	Location	Chr	Start/End	Methylation difference (%)	Methylation state	Gene expression in CD
IRGM	NS	promoter exon	chr5	150,846,720	29.52775476	Hyper	Up or downregulated variant dependent (Ajayi et al., 2019)
			chr5	150,846,746	29.991715	Hyper
			chr5	150,846,762	40.56338028	Hyper
	S	promoter exon	chr5	150,846,886	39.91304348	Hyper
CARD9	NS	promoter	chr9	136,374,386	−36.65546846	Hypo	Variant upregulated (Luo et al., 2020)
		intron	chr9	136,380,070	30.4981452	Hyper
			chr9	136,380,071	43.28063241	Hyper
MUC2	NS	intron	chr11	1,082,168	−33.29787234	Hypo	Up (Cari et al., 2023)
		exon	chr11	1,083,816	−30.85048754	Hypo
	S	intron	chr11	1,077,402	−44.58364038	Hypo
			chr11	1,081,571	−41.94444444	Hypo
			chr11	1,081,601	−45	Hypo
NOD2	NS	intron	chr16	50,719,712	−36.54051173	Hypo
	S	exon	chr16	50,715,637	37.36805067	Hyper
		intron	chr16	50,719,712	−63.60779384	Hypo
			chr16	50,719,717	−44.68887492	Hypo
TYK2	NS	intron	chr19	10,353,462	29.5194508	Hyper
	S	intergenic	chr19	1,0,381,760	34.47368421	Hyper
			chr19	10,388,056	−61.29032258	Hypo
DMRs mapped to CD linked genes
MUC4	NS	promoter exon intron	chr3	195,810,001/195,811,000	−61.7433	Hypo	Up (Dorofeyev et al., 2013; Li et al., 2023)
		exon intron	chr3	195,809,001/195,810,000	−54.7963	Hypo
	S	exon intron	chr3	195,809,001/195,810,000	−51.6707	Hypo
IL10RB	S	intron	chr21	33,290,001/33,291,000	−52.5686	Hypo
SLC15A1	S	intergenic	chr13	98,776,001/98,777,000	−51.5779	Hypo	Up (Ingersoll et al., 2012)
PIK3R2	NS	exon intron	chr19	18,155,001/18,156,000	−58.7821	Hypo
	S	exon intron	chr19	18,155,001/18,156,000	−51.2262	Hypo