Table 3.

Genetic association between four overlapping common SNPs identified in the HYPEST and CADCZ study groups and DNA methylation in the EGCUT sample set

SNP	Tested allele	CpG sitea	CpG position at chr. 16b	Distance between SNP and CpG (bp)	β (SE)c	95 % CI	P value	FDRc
rs8060301	A	cg09415485	82,663,111	1,367	−0.68 (0.06)	[−0.79, −0.57]	1.53 × 10−32	1.89 × 10−30
		cg19369556	82,661,725	19	−0.35 (0.07)	[−0.49, −0.20]	2.84 × 10−6	7.04 × 10−5
rs12444338	T	cg09415485	82,663,111	2,956	−0.57 (0.06)	[−0.70, −0.45]	8.53 × 10−19	5.29 × 10−17
		cg19369556	82,661,725	1,570	−0.31 (0.07)	[−0.46, −0.16]	3.35 × 10−5	6.92 × 10−4
rs12443878	A	cg09415485	82,663,111	3,178	−0.49 (0.07)	[−0.62, −0.35]	1.78 × 10−12	7.36 × 10−11
		cg19369556	82,661,725	1,792	−0.26 (0.08)	[−0.41, −0.11]	6.15 × 10−4	1.09 × 10−2
		cg09044981	82,827,677	167,744	0.26 (0.08)	[0.11, 0.41]	7.53 × 10−4	1.17 × 10−2
rs62040565	C	cg09415485	82,663,111	2,165	−0.39 (0.07)	[−0.53, −0.24]	1.10 × 10−7	3.40 × 10−6

SE standard error, CI confidence interval

^aCpG site ID on Infinium HumanMethylation450 BeadChip

^bGenomic position on chromosome 16 (GRCh37/hg19)

^cFalse discovery rate (FDR) corrected P value; only associations, significant after FDR correction, are given. Effects (tested allele effect on DNA methylation on transformed scale, see “Materials and methods”) and P values are calculated using linear regression