Table 1. The top-ranked CpG sites associated with coffee consumption in blood with/without smoking adjustment.

									PEG1 Caucasian Ctrl only, adjusted for age, gender, cell counts (subset1)		WHI Caucasian-only, adjusted for age, cell counts (subset2)		WHI Hispanic-only, adjusted for age, cell counts (subset3)		WHI African American-only, adjusted for age, cell counts (subset4)
	CpG	Gene	Chr.	Position (bp)a	Relation to UCSC CpG island	UCSC RefGene groupb	meta.Z	meta. P-value	biCor	P-value	biCor	P-value	biCor	P-value	biCor	P-value
(a) Adjusting for chronological age, gender, and blood cell counts
1	cg21566642	Intergenic, near ALPPL2	2	233284661	Island		−6.26	3.73E−10	−0.29	3.60E−05	−0.14	1.34E−05	−0.07	1.28E−01	−0.10	1.33E−02
2	cg20333292	GPR132	14	105532012		TSS1500	5.05	4.33E−07	0.28	7.43E−05	0.05	8.67E−02	0.13	6.87E−03	0.07	9.10E−02
3	cg21163128	BSCL2	11	62477362	Island	TSS1500	5.00	5.70E−07	0.28	6.77E−05	0.10	2.40E−03	0.09	6.23E−02	0.04	2.80E−01
4	cg23303782	GRK5	10	120967744	S_Shore	Body	4.81	1.49E−06	0.29	3.55E−05	0.06	4.37E−02	0.09	6.39E−02	0.06	1.14E−01
5	cg26105150	FSTL5	4	163085403		TSS1500	4.78	1.77E−06	0.27	1.35E−04	0.05	8.98E−02	0.16	6.78E−04	0.02	5.45E−01
6	cg19723563	PTHLH	12	28123034	Island	TSS200	4.74	2.13E−06	0.17	2.14E−02	0.07	2.20E−02	0.13	5.22E−03	0.08	3.77E−02
7	cg17928869	Intergenic, between EIF1 and KRT42P	17	39822542	S_Shore		4.68	2.86E−06	0.23	1.35E−03	0.08	1.17E−02	0.11	2.11E−02	0.05	1.93E−01
8	cg12866551	MALRD1	10	20019641			4.66	3.12E−06	0.23	1.48E−03	0.07	2.04E−02	0.14	2.75E−03	0.03	4.21E−01
9	cg15722372	PSMD8	19	38865020	N_Shore	TSS200	4.65	3.26E−06	0.20	4.55E−03	0.05	9.92E−02	0.10	4.67E−02	0.11	4.94E−03
10	cg19974428	TMEM130	7	98468047	Island	TSS1500	4.65	3.34E−06	0.22	2.29E−03	0.07	3.67E−02	0.11	2.64E−02	0.07	5.55E−02
11	cg15140902	FLJ22536	6	21667815	S_Shore	Body	4.60	4.14E−06	0.12	1.09E−01	0.10	1.52E−03	0.10	4.12E−02	0.09	1.72E−02
(b) Adjusting for chronological age, gender, blood cell counts, and smoking
1	cg21163128	BSCL2	11	62477362	Island	TSS1500	4.95	7.36E−07	0.30	1.87E−05	0.09	7.19E−03	0.09	6.96E−02	0.04	2.82E−01
2	cg08119527	Intergenic, near PODXL	7	131340667			4.84	1.28E−06	0.30	2.81E−05	0.09	4.68E−03	0.09	6.27E−02	0.03	4.44E−01
3	cg26331135	CNTN4	3	2144068	S_Shelf	5'UTR	4.71	2.46E−06	0.31	1.31E−05	0.04	1.92E−01	0.13	7.96E−03	0.04	2.91E−01
4	cg20333292	GPR132	14	105532012		TSS1500	4.62	3.85E−06	0.24	7.22E−04	0.06	8.21E−02	0.12	1.36E−02	0.06	1.04E−01
5	cg08311403	ROBO3	11	124735215	Island	TSS200	4.57	4.98E−06	0.16	3.04E−02	0.07	3.16E−02	0.06	2.48E−01	0.14	2.67E−04

Abbreviations: ALPPL2, alkaline phosphatase, placental-like 2; BSCL2, Berardinelli–Seip congenital lipodystrophy 2 (seipin); CNTN4, Contactin 4; EIF1, eukaryotic translation initiation factor 1; FLJ22536, miscRNA; FSTL5, follistatin-like 5; GPR132, G Protein-Coupled Receptor 132; GRK5, G protein-coupled receptor kinase 5; KRT42P, keratin 42 pseudogene; MALRD1, MAM and LDL receptor class A domain containing 1; PODXL, podocalyxin-like; PSMD8, proteasome (prosome, macropain) 26 S subunit, non-ATPase, 8; PTHLH, parathyroid hormone-like hormone; ROBO3, roundabout guidance receptor 3; TMEM130, transmembrane protein 130; TSS, transcription start site; UTR, untranslated region.

List of CpGs associated with coffee consumption, (in/near) gene, chromosome, and CpG island location, gene region, (Stouffer's test) Z-value and P-value from meta-analysis, a robust correlation coefficient (known as biweight midcorrelation) and P-value for daily coffee consumption (in last 3 months in WHI or 12 months in PEG1) and DNA methylation levels within four population subsets.

^aLocation is based on NCBI genome build 37.

^bTSS500: within 1500 bps of a TSS, TSS200: within 200 bps of a TSS.