Do changes in DNA methylation mediate or interact with SNP variation? A pharmacoepigenetic analysis

BMC Genomic Data

Table 1 Top 5 most significant NIEs

SNP	CpG	SNP MAF	Chr	Distance	TE	TE p value	NDE	NDE p value	NIE	NIE p value
rs12771141	cg04855826	0.359	10	12.5	0.071	3.12E − 03	1.745	0.048	0.008	0.068
rs12438405	cg21284575	0.436	15	28.8	0.064	5.29E − 03	−3.036	0.135	0.008	0.068
rs6832151	cg15003695	0.283	4	19.6	−0.074	2.77E − 03	5.253	0.008	−0.008	0.084
rs32458	cg12200124	0.329	5	39.3	0.049	0.03217	−0.272	0.398	0.007	0.088
rs11634929	cg03678138	0.041	15	8.7	−0.234	4.51E-04	−6.022	0.030	−0.054	0.089

Distance between SNP and CpG site is reported in kilobases. The natural direct effect (NDE) refers to the SNP effect that is not mediated by change in methylation. This is estimated by the coefficient θ₁ from model (2). The total effect (TE) is the SNP effect γ₁ in the unadjusted regression model (3)
MAF minor allele frequency

ISSN: 2730-6844