Table 2.

Top smoking-associated CpGs in GTEx lung and colon samples (based on p value)

Tissue	Annotated genea(or region)	Chr:Position	CpG	p value	CpGs passing FDRb	Region identified previously	Other tissues (FDR 0.05)	Association withexpression (p value)
Lung	EDC3	15:74935742	cg26843110	2.61E-25	4	yes	no	up (5.63E-12)
	HIPK2	7:139420300	cg03224163	3.70E-23	4	yes	colon	down (0.05)
	AHRR	5:346695	cg04135110	6.97E-22	66	yes	colon	up (1.08E-46)
	CYP1A1c	15:75015502	cg23655854	8.26E-22	18	yes	colon	up (3.08E-17)
	AOPEPd	9:97544885	cg21081352	1.79E-19	5	no	colon	no
	5p15.33	5:1128194	cg03504128	3.76E-19	1	no	no	N/A
	LRP5	11:68079135	cg04840942	1.70E-17	15	yes	colon	no
	PLA2G4E	15:42313231	cg16167478	2.47E-17	6	no	no	up (2.61E-12)
	NOTCH1	9:139416102	cg14120703	1.04E-16	2	yes	no	down (0.04)
	CYP1B1	2:38296474	cg01584760	2.83E-16	10	yes	colon	up (1.90E-16)
Colon	AHRR	5:374252	cg04141806	2.85E-12	17	yes	lung	up (2.31E-7)
	GPR55e	2:231809610	cg08840017	7.61E-12	1	yes	no	up (6.31E-6)
	HIPK2	7:139366758	cg25748521	4.40E-11	2	yes	lung	no
	RHOU	1:228871677	cg27437294	1.73E-10	2	no	no	no
	WNK2	9:95947164	cg10281741	1.99E-10	5	no	no	no
	FAM184B	4:17783205	cg01886556	4.88E-10	4	yes	no	no
	LAMA3	18:21269793	cg25009504	7.59E-10	3	no	no	no
	NRP1	10:33624100	cg09009410	1.35E-09	4	no	lung	no
	NHLH2	1:116381475	cg24106636	3.17E-09	2	no	no	N/A
	DIP2C	10:735472	cg25488288	3.54E-09	2	yes	no	no

^aBased on Illumina’s annotation for the EPIC array. Cytoband is listed if there is no annotated gene.

^bThe number CpGs passing FDR (0.05) that are annotated to the gene listed (based on Illumina’s annotation).

^cCYP1A1 and EDC3 are in the same region, separated by < 25 kb.

^dAOPEP is also known as C9ORF3.

^eCpG cg08840017 was assigned to GPR55 as it resides in a GRP55 isoform.