Table 2.

Top 1% (n = 12) of Ranked Hypo- and Hypermethylated CpGs from EPIC HD. BH: Benjamini Hochberg, hg19: human genome assembly 19.

EPIC HD Top Hypomethylated CpGs
Eank	450K Probe	Genomic Location (hg19)	Closest Coding Element	Distance to Closest TSS [bp]	EPIC HD Mean Methylation Difference [%]	EPIC HD BH p-Value	TCGA SCC Mean Methylation Difference [%]	TCGA SCC FDR p-Value	TCGA ADC Mean Methylation Difference [%]	TCGA ADC FDR p-Value
1	cg22586603	chr8:129985596	LINC00976	7350	−8.9	2.7 × 10−2	−22.1	1.9 × 10−12	−11.9	2.0 × 10−4
2	cg13291208	chr8:70475388	SULF1	29,757	−6.6	3.6 × 10−2	−18.2	1.3 × 10−6	−23.4	1.2 × 10−8
3	cg06126421	chr6:30720080	IER3	7753	−6.3	2.4 × 10−2	−17.3	1.5 × 10−8	−4.4	3.7 × 10−1
4	cg13204432	chr2:51074939	NRXN1	184,735	−4.1	1.6 × 10−7	−9.1	4.5 × 10−12	−8.5	4.9 × 10−6
5	cg05951044	chr18:23597141	SS18	73,470	−4.1	2.7 × 10−4	−8.7	1.2 × 10−6	−3.6	4.2 × 10−2
6	cg04955914	chr2:220040571	CNPPD1	1144	−3.9	2.1 × 10−3	−6.0	5.0 × 10−3	−7.1	3.3 × 10−2
EPIC HD Top Hypermethylated CpGs
Rank	450K Probe	Genomic Location (hg19)	Closest Coding Element	Distance to Closest TSS [bp]	EPIC HD Mean Methylation Difference [%]	EPIC HD BH p-Value	TCGA SCC Mean Methylation Difference [%]	TCGA SCC FDR p-Value	TCGA ADC Mean Methylation Difference [%]	TCGA ADC FDR p-Value
1	cg06646708	chr6:18123224	NHLRC1	374	6.7	3.2 × 10−2	−29.3	6.3 × 10−25	−23.9	2.5 × 10−18
2	cg17242351	chr15:35086890	ACTC1	1037	6.6	1.7 × 10−3	22.9	1.0 × 10−8	22.0	1.7 × 10−10
3	cg07714266	chr7:28075371	JAZF1	145,066	5.5	7.7 × 10−3	−14.4	4.5 × 10−11	−2.1	1.9 × 10−1
4	cg26484090	chr6:99960583	USP45	2669	5.4	2.0 × 10-2	−3.2	2.7 × 10−3	−1.2	3.2 × 10−1
5	cg00554165	chr5:172536348	CREBRF	52,993	5.2	4.7 × 10−3	4.6	1.7 × 10−5	0.2	5.8 × 10−1
6	cg14187813	chr2:97651611	FAM178B	690	4.9	3.6 × 10−3	−15.2	9.9 × 10−9	3.0	5.3 × 10−1