Table 2.

Differentially Methylated CpGs with Best Discriminatory Performance and Good Correlation with GE

Gene	CHR	CpG	Gene location	CpG location	ME			GE			Correlation of ME-GE
					Direction	Δβ Methylation	P value	Direction	Fold change	P value	r	P value
HLA-F	6	cg12588917	Body	Island	Hyper	0.145	1.2 × 10−11	Down	−1.246	0.001	−0.631	0
		cg24351901	Body	Island	Hyper	0.144	2.4 × 10−9
		cg15331332	Body	Shore	Hyper	0.142	6.7 × 10−9
		cg23892836	Body	Island	Hyper	0.129	3.5 × 10−9
		cg07016276	Body	Island	Hyper	0.101	4.6 × 10−6
		cg00504902	Body	Shore	Hyper	0.102	2.2 × 10−6
SLFN12	17	cg19566405	TSS1500	Opensea	Hyper	0.130	2.2 × 10−8	Down	−1.223	0.000	−0.583	0
		cg05174890	TSS1500	Opensea	Hyper	0.113	7.4 × 10−7
		cg11346248	TSS1500	Opensea	Hyper	0.110	6.8 × 10−8
		cg03251655	First exon	Opensea	Hyper	0.100	1.5 × 10−7
		cg21697381	TSS1500	Opensea	Hyper	0.100	7.5 × 10−8
HLA-DMA	6	cg02806715	Body	Opensea	Hyper	0.126	1.0 × 10−11	Down	−1.276	0.000	−0.578	0
		cg24129356	First exon	Opensea	Hyper	0.121	5.3 × 10−11
UBE2L6	11	cg27429749	Body	Shore	Hyper	0.117	2.2 × 10−6	Down	−1.193	0.038	−0.521	7.3 × 10−11
ANK3	10	cg14274656	First exon	Opensea	Hypo	−0.117	3.0 × 10−6	Down	−1.140	0.033	−0.409	1.0 × 10−6
		cg16134349	First exon	Opensea	Hypo	−0.104	5.0 × 10−8
BST2	19	cg11558551	TSS200	Opensea	Hyper	0.102	5.0 × 10−8	Down	−1.361	0.000	−0.380	6.0 × 10−6
HLA-DPA1	6	cg12858166	3′UTR	Opensea	Hyper	0.104	1.1 × 10−2	Down	−1.198	0.003	−0.315	2.0 × 10−4

CHR, chromosome; GE, gene expression; Hyper, hypermethylation; Hypo, hypomethylation; ME, gene methylation; TSS, transcription start site; UTR, untranslated region.