DNA methylation and lipid metabolism: an EWAS of 226 metabolic measures

Clinical Epigenetics

Table 2 Results of gene expression analysis of CpG sites associated with metabolic measures

CpG site	CHR	Probe ID	CpG annotated gene	Transcript annotated gene	Distance	Beta value	P	P Bonferroni	N	Tissue
cg16246545	1	ILMN_1704537	PHGDH	PHGDH	0	− 2.77	1.44e−24	6.91e−22	634	Whole blood
cg24503796	10	ILMN_1689329	SCD	SCD	0	− 1.45	2.39e−08	1.15e−05	633	Whole blood
cg03440556	10	ILMN_1689329	SCD	SCD	0	− 0.57	7.43e−07	3.56e−4	609	Whole blood
cg06500161	21	ILMN_2329927	ABCG1	ABCG1	0	− 2.79	2.67e−07	1.28e−4	635	Whole blood
cg20544516	17	ILMN_1663035	SREBF1	SREBF1	1542	− 0.38	8.83e−10	4.59e−07	626	Subcutaneous fat
cg20544516	17	ILMN_1745806	SREBF1	PEMT	308200	0.27	1.64e−05	8.53e−3	626	Subcutaneous fat
cg20544516	17	ILMN_1811933	SREBF1	SHMT1	514197	− 0.37	2.85e−09	1.48e−6	626	Subcutaneous fat
cg20544516	17	ILMN_2328986	SREBF1	SREBF1	1208	− 0.28	1.26e−05	6.57e−3	626	Subcutaneous fat

Statistically significant associations between metabolic measure-associated CpG sites and expression of cis-transcripts in whole blood (KORA F4, Bonferroni-adjusted significance threshold p < 0.05/480 = 1.0e−4) and subcutaneous fat (TwinsUK study, p < 0.05/521 = 9.6e−5). “Probe ID” and “Transcript_annotated_gene” are the transcript ID and annotated gene from the Illumina annotation files; CHR: chromosome location of the CpG site; distance: distance between the CpG site and the transcript based on positions given in the annotation files; beta value: beta-coefficient; P: p value; P Bonferroni: Bonferroni-corrected p value; N: number of observations in the model. All coefficients are change in log2-transformed expression intensity per unit increase in methylation (beta value on 0–1 scale), except for subcutaneous fat, which is correlation assessed using the R-package rmcorr

ISSN: 1868-7083