Table 2.

Functional analysis of HCV-HCC-associated dmRE in TCGA

RE type	RE location (hg19)a	Proximal gene symbol	Distance to proximal gene (bp)	Genomic region	Differential methylation analysis (HCV-HCC vs normal)		RE methylation vs gene expression correlation analysis		Differential gene expression analysis (HCV-HCC vs normal)		Directionally consistent
					Mean difference	p value	Max. Correlationb	Min. p valueb	log2 fold change	p value
LINE-1	chr10:134875427–134876211	ADGRA1	25,296	Intergenic	− 0.331	6.97E−07	− 0.23	0.613	− 3.358	0.004	No
LINE-1	chr6:9810984–9817010	N/A c	N/Ac	Intergenic	− 0.203	1.23E−06	N/Ac	N/Ac	N/Ac	N/Ac	N/Ac
LINE-1	chr7:4388884–4389235	SDK1	80,252	Intergenic	− 0.382	1.08E−07	0.62	0.008	− 0.018	0.980	Yes
LINE-1	chr7:4085177–4085587	SDK1	0	Intronic	− 0.365	3.29E−06	0.33	0.161	− 0.018	0.980	Yes
LINE-1	chr7:157594780–157595648	PTPRN2	0	Intronic	− 0.385	4.40E−05	0.72	0.004	− 1.053	0.116	Yes
LINE-1	chr11:2499185–2499531	KCNQ1	0	Intronic	− 0.408	1.83E−05	0.53	0.034	1.343	0.076	No
LINE-1	chr5:8084329–8090357	MTRR	183,093	Intergenic	− 0.168	1.47E−05	−0.51	0.044	0.062	0.866	Yes
LINE-1	chr2:242938503–242938722	LINC01237	0	Intronic	− 0.337	1.18E−05	0.28	0.274	0.764	0.344	No
LINE-1	chr7:157318533–157319261	PTPRN2	12,488	Intergenic	− 0.443	2.19E−09	0.67	0.003	− 1.053	0.116	Yes
LINE-1	chr8:142852678–142853054	MROH5	335,347	Intergenic	− 0.409	2.99E−05	−0.54	0.269	0.573	0.737	Yes
LINE-1	chr8:143458657–143458848	TSNARE1	0	Intronic	0.107	2.73E−05	0.58	0.020	0.960	0.013	Yes
LINE-1	chr2:1166233–1166668	SNTG2	0	Intronic	− 0.276	1.44E−05	0.82	0.047	− 0.102	0.955	Yes
Alu	chr13:30062564–30062769	MTUS2	0	Intronic	− 0.275	9.85E−07	0.52	0.156	− 3.564	0.335	Yes
Alu	chrX:103294139–103294294	H2BFM	222	Promoterd	− 0.390	1.13E−06	N/Ae	N/Ae	N/Ae	N/Ae	N/Ae
Alu	chr6:31598686–31598816	PRRC2A	0	Intronic	0.137	2.90E−06	0.25	0.284	1.089	0.001	Yes

^aRanked by statistical significance, within LINE-1 and Alu, respectively

^bMaximum magnitude of correlation and minimum p values across the CpGs in the RE

^cNo proximal gene identified within 500 kbp

^dWithin 2000 bp upstream of the transcription start site

^eExtremely low expression across samples