Table 2.

CpG sites differentially methylated in relation to smoking in the discovery cohort. The CpG id, associated gene or transcript, chromosome (chr) location, genomic position, and observed mean β-values (standard deviation) across smoking defined groups are shown.

CpG	Annotated Gene (Nearest Gene)	Chr	Position	Current Smokers N = 107	Former Smokers 1 to 5 y N = 31	Former Smokers >5 y N = 165	Never Smokers N = 342	P-value(current vs. never smokers)	P-value (considering all 4 groups)
cg04885881	NA (SRM)	1	11123118	0.420 (0.005)	0.424 (0.010)	0.446 (0.004)	0.458 (0.003)	6.85E-09	4.51E-09
cg27537125	NA (MIR4425)	1	25349681	0.184 (0.003)	0.190 (0.005)	0.197 (0.002)	0.205 (0.002)	4.34E-11	6.01E-11
cg25189904	GNG12	1	68299493	0.408 (0.007)	0.403 (0.013)	0.430 (0.006)	0.469 (0.004)	8.26E-14	1.65E-14
cg09662411	GFI1	1	92946132	0.738 (0.005)	0.757 (0.008)	0.756 (0.004)	0.764 (0.003)	2.86E-08	8.38E-07
cg06338710	GFI1	1	92946187	0.824 (0.003)	0.824 (0.006)	0.832 (0.003)	0.839 (0.002)	7.42E-08	2.00E-06
cg18146737	GFI1	1	92946700	0.908 (0.006)	0.910 (0.010)	0.923 (0.005)	0.929 (0.003)	8.50E-10	4.50E-08
cg12876356	GFI1	1	92946825	0.756 (0.006)	0.776 (0.010)	0.780 (0.004)	0.795 (0.003)	9.02E-13	2.12E-11
cg18316974	GFI1	1	92947035	0.911 (0.004)	0.920 (0.006)	0.928 (0.003)	0.932 (0.002)	1.18E-12	3.75E-11
cg08709672	AVPR1B	1	206224334	0.596 (0.003)	0.611 (0.006)	0.615 (0.003)	0.617 (0.002)	2.15E-08	5.55E-07
cg03547355	NA (PSEN2)	1	227003060	0.567 (0.004)	0.567 (0.007)	0.574 (0.003)	0.591 (0.002)	2.21E-08	2.56E-09
cg23079012	LINC00299	2	8343710	0.939 (0.002)	0.949 (0.003)	0.951 (0.001)	0.955 (0.001)	6.54E-14	6.06E-13
cg26271591	NFE2L2	2	178125956	0.353 (0.005)	0.368 (0.009)	0.380 (0.004)	0.395 (0.003)	4.32E-12	3.95E-11
cg27241845	NA (ECEL1P2)	2	233250370	0.608 (0.004)	0.608 (0.008)	0.628 (0.004)	0.644 (0.002)	3.02E-12	8.71E-12
cg03329539	NA (ALPPL2; ACO68134.6)	2	233283329	0.353 (0.004)	0.360 (0.008)	0.377 (0.003)	0.397 (0.002)	7.34E-18	2.04E-18
cg06644428	NA (ALPPL2; ACO68134.6)	2	233284112	0.074 (0.003)	0.079 (0.006)	0.087 (0.003)	0.111 (0.002)	2.51E-23	6.02E-26
cg05951221	NA (ALPPL2; ACO68134.6)	2	233284402	0.344 (0.006)	0.371 (0.011)	0.397 (0.005)	0.454 (0.003)	2.35E-48	4.90E-51
cg21566642	NA (ALPPL2; ACO68134.6)	2	233284661	0.372 (0.006)	0.417 (0.012)	0.457 (0.005)	0.512 (0.004)	2.74E-60	6.45E-63
cg01940273	NA (ALPPL2; ACO68134.6)	2	233284934	0.559 (0.005)	0.595 (0.009)	0.615 (0.004)	0.647 (0.003)	8.70E-42	5.56E-43
cg13193840	NA (ALPPL2; ACO68134.6)	2	233285289	0.121 (0.002)	0.120 (0.004)	0.129 (0.002)	0.136 (0.001)	1.94E-08	1.48E-08
cg19859270	GPR15	3	98251294	0.848 (0.002)	0.851 (0.003)	0.859 (0.002)	0.869 (0.001)	7.03E-21	1.59E-21
cg12806681	AHRR	5	368394	0.85 (0.003)	0.847 (0.005)	0.866 (0.002)	0.869 (0.002)	4.59E-09	1.45E-10
cg03991871	AHRR	5	368447	0.807 (0.004)	0.800 (0.008)	0.836 (0.003)	0.842 (0.002)	4.08E-13	3.02E-15
cg23916896	AHRR	5	368804	0.245 (0.006)	0.252 (0.010)	0.271 (0.005)	0.290 (0.003)	5.93E-11	1.14E-10
cg11902777	AHRR	5	368843	0.077 (0.002)	0.080 (0.004)	0.089 (0.002)	0.096 (0.001)	1.27E-13	2.17E-12
cg05575921	AHRR	5	373378	0.685 (0.006)	0.755 (0.011)	0.810 (0.005)	0.850 (0.003)	4.11E-84	1.27E-84
cg14817490	AHRR	5	392920	0.259 (0.005)	0.283 (0.008)	0.291 (0.004)	0.306 (0.003)	3.23E-17	5.73E-16
cg17287155	AHRR	5	393347	0.848 (0.003)	0.854 (0.005)	0.863 (0.002)	0.869 (0.001)	3.59E-12	2.72E-11
cg04551776	AHRR	5	393366	0.757 (0.003)	0.766 (0.006)	0.777 (0.003)	0.782 (0.002)	3.58E-11	5.46E-10
cg25648203	AHRR	5	395444	0.758 (0.003)	0.784 (0.006)	0.79 (0.003)	0.794 (0.002)	1.09E-19	1.27E-18
cg21161138	AHRR	5	399360	0.677 (0.004)	0.694 (0.007)	0.714 (0.003)	0.725 (0.002)	9.28E-23	1.96E-21
cg14580211	C5orf62	5	150161299	0.645 (0.005)	0.671 (0.009)	0.664 (0.004)	0.680 (0.003)	7.20E-09	5.17E-08
cg12513616	LOC728554	5	177370977	0.440 (0.004)	0.443 (0.008)	0.453 (0.004)	0.467 (0.002)	4.05E-08	3.63E-07
cg06126421	NA (IR3; RN7SL353P)	6	30720080	0.598 (0.007)	0.621 (0.012)	0.654 (0.005)	0.700 (0.004)	6.69E-38	1.65E-36
cg14753356	NA (IR3; RN7SL353P)	6	30720108	0.366 (0.005)	0.386 (0.010)	0.385 (0.004)	0.406 (0.003)	8.29E-11	1.69E-09
cg24859433	NA (IR3; RN7SL353P)	6	30720203	0.787 (0.003)	0.795 (0.005)	0.808 (0.002)	0.817 (0.002)	4.12E-17	5.86E-16
cg15342087	NA (IR3; RN7SL353P)	6	30720209	0.780 (0.003)	0.791 (0.006)	0.803 (0.002)	0.811 (0.002)	3.64E-18	6.20E-17
cg22132788	MYO1G	7	45002486	0.895 (0.006)	0.882 (0.011)	0.879 (0.005)	0.858 (0.003)	4.98E-10	1.90E-09
cg12803068	MYO1G	7	45002919	0.756 (0.009)	0.736 (0.016)	0.736 (0.007)	0.702 (0.005)	5.07E-08	4.38E-08
cg11556164	LRRN3	7	110738315	0.723 (0.004)	0.726 (0.006)	0.736 (0.003)	0.746 (0.002)	4.94E-08	6.23E-08
cg05221370	LRRN3	7	110738836	0.178 (0.003)	0.185 (0.006)	0.197 (0.003)	0.206 (0.002)	1.47E-11	9.21E-12
cg21322436	CNTNAP2	7	145812842	0.261 (0.004)	0.284 (0.006)	0.285 (0.003)	0.296 (0.002)	3.91E-16	9.81E-16
cg25949550	CNTNAP2	7	145814306	0.139 (0.003)	0.150 (0.005)	0.153 (0.002)	0.163 (0.001)	2.37E-14	8.83E-14
cg11207515	CNTNAP2	7	146904205	0.423 (0.007)	0.390 (0.012)	0.394 (0.005)	0.379 (0.004)	6.70E-08	2.31E-06
cg24540678	ZNF395	8	28258603	0.196 (0.003)	0.209 (0.006)	0.209 (0.003)	0.219 (0.002)	6.50E-10	1.80E-08
cg24838345	MTSS1	8	125737353	0.757 (0.004)	0.775 (0.007)	0.772 (0.003)	0.782 (0.002)	9.08E-08	3.58E-07
cg12075928	PTK2	8	141801307	0.479 (0.005)	0.465 (0.009)	0.494 (0.004)	0.515 (0.003)	8.73E-10	1.07E-12
cg26361535	ZC3H3	8	144576604	0.695 (0.006)	0.724 (0.010)	0.716 (0.005)	0.736 (0.003)	2.67E-09	1.48E-08
cg01692968	NA (SLC44A1)	9	108005349	0.320 (0.005)	0.339 (0.009)	0.332 (0.004)	0.35 (0.003)	7.14E-08	6.75E-07
cg03450842	ZMIZ1	10	80834947	0.563 (0.004)	0.580 (0.007)	0.584 (0.003)	0.589 (0.002)	1.14E-08	1.42E-07
cg05329352	ADRA2A	10	112838983	0.565 (0.006)	0.603 (0.011)	0.584 (0.005)	0.603 (0.003)	8.35E-08	3.42E-07
cg26963277	KCNQ1OT1; KCNQ1	11	2722407	0.872 (0.003)	0.879 (0.005)	0.887 (0.002)	0.893 (0.002)	1.04E-10	6.53E-09
cg21611682	LRP5	11	68138269	0.536 (0.004)	0.549 (0.007)	0.559 (0.003)	0.567 (0.002)	5.68E-10	3.95E-09
cg14624207	LRP5	11	68142198	0.517 (0.004)	0.526 (0.007)	0.529 (0.003)	0.542 (0.002)	7.14E-08	4.01E-07
cg01901332	ARRB1	11	75031054	0.611 (0.005)	0.628 (0.008)	0.640 (0.004)	0.649 (0.003)	7.19E-12	1.71E-10
cg11660018	PRSS23	11	86510915	0.505 (0.005)	0.525 (0.009)	0.526 (0.004)	0.549 (0.003)	1.26E-12	2.04E-12
cg23771366	PRSS23	11	86510998	0.422 (0.005)	0.437 (0.010)	0.441 (0.004)	0.458 (0.003)	1.46E-08	2.02E-07
cg02583484	HNRNPA1	12	54677008	0.310 (0.004)	0.328 (0.007)	0.325 (0.003)	0.340 (0.002)	9.11E-11	1.90E-10
cg06394460	LNX2	13	28130393	0.566 (0.006)	0.606 (0.011)	0.601 (0.005)	0.609 (0.003)	5.35E-09	6.65E-08
cg05284742	ITPK1	14	93552128	0.695 (0.003)	0.707 (0.006)	0.714 (0.003)	0.721 (0.002)	3.75E-10	7.03E-09
cg05886626	THBS1	15	39873553	0.207 (0.004)	0.218 (0.007)	0.222 (0.003)	0.230 (0.002)	8.41E-08	5.18E-06
cg23161492	ANPEP	15	90357202	0.254 (0.005)	0.274 (0.009)	0.280 (0.004)	0.296 (0.003)	2.23E-12	7.53E-11
cg01207684	ADCY9	16	4103167	0.711 (0.005)	0.717 (0.010)	0.732 (0.004)	0.745 (0.003)	3.13E-08	7.98E-08
cg19572487	RARA	17	38476024	0.488 (0.005)	0.484 (0.009)	0.511 (0.004)	0.535 (0.003)	9.46E-14	7.54E-16
cg07381806	MOBKL2A	19	2094327	0.344 (0.006)	0.372 (0.012)	0.374 (0.005)	0.382 (0.004)	1.06E-07	8.89E-06
cg03636183	F2RL3	19	17000585	0.607 (0.005)	0.636 (0.009)	0.671 (0.004)	0.706 (0.003)	6.28E-49	4.07E-50
cg07339236	ATP9A	20	50312490	0.155 (0.003)	0.179 (0.006)	0.174 (0.003)	0.185 (0.002)	2.09E-14	1.70E-13

NA: Non-annotated gene (nearest gene); All P-values were calculated using M-values