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

BMC Genomic Data

Table 2 Top 5 most significant interaction effects

SNP	CpG	SNP MAF	Chr	Distance	TE	TE p value	Int. effect	Int. p value	NIE	NIE p value
rs4686740	cg21463380	0.482	3	40.8	3.12E − 03	7.64E − 03	1.025	6.11E − 09	0.005	0.144
rs2575	cg21463380	0.482	3	47.2	5.29E − 03	9.14E − 03	0.980	3.02E − 08	0.006	0.091
rs17216446	cg15395354	0.458	4	19.0	2.77E − 03	8.50E − 04	0.624	1.41E − 06	0.003	0.257
rs1997579	cg12299303	0.118	21	39.0	0.03217	3.85E − 05	−1.339	8.95E − 04	−0.004	0.328
rs1143115	cg17140441	0.439	15	27.8	4.51E-04	3.74E − 04	0.383	1.56E − 03	0.002	0.268

Distance between SNP and CpG site in kilobases, NIE, and total genetic effects (TE) from the unadjusted model are also reported
Int interaction, MAF minor allele frequency

ISSN: 2730-6844