Table 1. CpG site differences from EPIC array and the BSAS methods at the 15 loci of differing levels of significance (not significant, nominally significant, and significant after P-value adjustment).

				Illumina EPIC array			BSAS			Difference between methods
	Cg/Gene	Position in genome	Illumina ID	β difference	P value	FDR Adjusted P value	β difference	P value	FDR Adjusted P value	β difference
1	AHRR	Chr5, GB	cg05575921	−0.233	5.33E−12	3.7E−06	−0.041	0.006	0.245	−0.192
2	cg11977356a	Chr19	cg11977356	−0.040	0.474	0.999	−0.004	0.406	0.959	−0.036
3	ITPR1	Chr3, GB	cg08987995	−0.001	0.572	0.999	0.005	0.820	0.822	−0.006
4	MAGI	Chr7, GB	cg21121803	−0.008	0.572	0.999	−0.007	0.809	0.959	−0.0004
5	EHMT2	Chr6, GB	cg07829740	0.005	0.037	0.999	−0.015	0.071	0.579	0.020
6	PPM1L	Chr3, GB	cg26406186	−0.006	0.818	0.999	0.011	0.904	0.963	−0.017
7	cg00571101a	Chr12	cg00571101	0.004	0.368	0.999	−0.004	0.813	0.952	0.008
8	cg09078959a	Chr5	cg09078959	−0.001	0.893	0.999	−0.005	0.001	0.245	0.004
9	cg01614625a	Chr7	cg01614625	−0.009	0.370	0.999	−0.006	0.569	0.952	−0.004
10	DP10	Chr2, GB	cg05868547	0.006	0.077	0.999	−0.003	0.713	0.952	0.009
11	cg11293828a	Chr12	cg11293828	−0.014	0.665	0.999	0.032	0.735	0.952	−0.045
12	CHD7	Chr5, 5′UTR	cg19926587	−0.007	0.960	0.999	−0.006	0.429	0.959	−0.001
13	NIPAL4	Chr5, TSS1500	cg17695979	−0.007	0.714	0.999	−0.003	0.106	0.713	−0.004
14	PRDM5	Chr4, GB	cg01118724	−0.004	0.734	0.999	0.005	0.116	0.713	−0.009
15	SLC17A7	Chr19, GB	cg02624701	−0.043	0.312	0.999	0.018	0.646	0.952	−0.061

Notes.

^aWhen a cg number is listed, then there is no known gene associated with that CpG site. GB-Gene Body.