Table 1.

Top 10 hypermethylated and hypomethylated regions between HCC and NASH in the choline deficient model

	Chromosome	Start	End	Q-value	Methylation difference (%)	Gene	CpG Category	Gene Structure
Hypermethylation	Chr 8	3517616	3517616	1.65E-48	76.2212	PNPLA6	Shore	Exon
	Chr 17	32105855	32105855	8.63E-47	68.636	–	Other	–
	Chr 11	99645764	99645764	5.30E-74	67.33949	KRTAP4–7	Other	–
	Chr 5	129557719	129557719	4.11E-59	65.9518	CHCHD2	Other	Exon
	Chr 5	142945496	142945496	1.39E-55	65.23347	FSCN1	Other	–
	Chr 3	41581453	41581453	2.32E-44	64.13043	JADE1	Other	Exon
	Chr 9	121792412	121792412	5.80E-53	62.74613	–	Other	Intron
	Chr 4	155781218	155781218	4.83E-39	62.30984	TMEM88B	Other	Intron
	Chr 6	31666012	31666012	1.21E-81	62.05207	Gm13848	Other	Exon
	Chr 18	82756567	82756567	7.26E-80	61.81989	–	Other	Intergenic
Hypomethylation	Chr 2	30100458	30100458	3.98E-61	−68.875	ZDHHC12	Other	Intron
	Chr 2	170791632	170791632	8.07E-49	−67.2973	–	Other	Intron
	Chr 10	69846110	69846110	8.28E-53	−66.5238	GM33416	Other	Intron
	Chr 9	57968665	57968665	1.39E-36	−63.029	MYO5B	Other	Intron
	Chr 4	110051897	110051897	5.55E-47	−62.4214	DMRTA2	Shore	–
	Chr 16	97823834	97823834	1.62E-34	−61.5291	–	Other	Intron
	Chr 4	134744349	134744349	5.94E-31	−60.3271	LDLRAP1	Other	Exon
	Chr 7	36873554	36873554	7.09E-53	−59.9929	–	Other	–
	Chr 7	42750002	42750002	3.33E-34	−59.3331	DOCK3	Other	Exon
	Chr 5	74960682	74960682	4.97E-51	−59.0323	Gm6116	Other	Intron

Abbreviation: Chr Chromosome