. Author manuscript; available in PMC: 2017 Dec 12.

Published in final edited form as: Nat Genet. 2017 Jun 12;49(7):1126–1132. doi: 10.1038/ng.3892

Table 2.

The association between sentinel variants representing each lung cancer locus and lung cancer risk.

Strata	Locus^*	rs number	Gene	Allele^a	Imputed versus Oncoarray genotyped	Candidate Oncoarray	EAF	OR	95%CI	P-value	CPD	FTND	FEV1	FVC	FEV1/FVC
Strata	Locus^*	rs number	Gene	Allele^a	Imputed versus Oncoarray genotyped	Customized panel	EAF	OR	95%CI	P-value	p- value	p- value	p- value	p- value	p- value
Lung	1p31.1^*	rs71658797	FUBP1	T_A	Oncoarray	No	0.103	1.1	1.09–1.18	3.3E-11	0.056	0.334	0.445	0.898	0.334
Lung	6q27^*	rs6920364	RNASET2	G_C	Imputed	eQTL	0.456	1.1	1.05–1.10	1.3E-08	0.833	0.104	0.927	0.876	0.986
Lung	8p21.1^*	rs11780471	CHRNA2	G_A	Imputed	Lung	0.060	0.9	0.83–0.91	1.7E-08	0.646	0.403	6.9E-04	0.055	0.016
Lung	13q13.1	rs11571833	BRCA2	A_T	Imputed	Lung	0.011	1.6	1.43–1.80	6.1E-16	0.890	0.312	0.601	0.667	0.237
Lung	15q21.1^*	rs66759488	SEMA6D	G_A	imputed	Lung	0.362	1.1	1.05–1.10	2.8E-08	0.266	0.888	0.739	0.200	0.202
Lung	15q25.1	rs55781567	CHRNA5	C_G	Imputed	Lung	0.367	1.3	1.27–1.33	3.1E-103	6.8E-38	9.7E-16	7.2E-03	0.020	0.144
Lung	19q13.2^ˆ	rs56113850	CYP2A6	C_T	Oncoarray	Lung	0.440	0.9	0.86–0.91	5.0E-19	8.1E-20	7.5E-04	0.822	0.826	0.319
Adeno	3q28	rs13080835	TP63	G_T	Imputed	Lung	0.493	0.9	0.87–0.92	7.5E-12	0.803	0.336	0.135	0.445	0.834
Adeno	5p15.33	rs7705526	TERT	C_A	Oncoarray	All	0.342	1.3	1.21–1.29	3.8E-35	0.511	0.738	0.292	0.038	0.657
Adeno	8p12^*	rs4236709	NRG1	A_G	Imputed	eQTL	0.218	1.1	1.09–1.18	1.3E-10	0.991	0.957	0.503	0.151	0.403
Adeno	9p21.3^*	rs885518	CDNK2A	A_G	Imputed	Several	0.101	1.2	1.11–1.23	9.96E-10	0.904	0.321	0.421	0.096	0.146
Adeno	10q24.3^*	rs11591710	OBFC1	A_C	Imputed	Lung	0.137	1.2	1.11–1.22	6.3E-11	0.500	0.152	0.027	0.019	0.533
Adeno	11q23.3^*	rs1056562	AMICA1	C_T	Oncoarray	Breast	0.473	1.1	1.07–1.14	2.8E-10	0.717	0.538	0.449	0.718	0.039
Adeno	15q21.1^*	rs77468143	SECISBP2L	T_G	Imputed	No	0.253	0.9	0.83–0.89	1.7E-16	0.071	0.184	4.9E-03	0.440	1.4E-03
Adeno	20q13.33^*	rs41309931	RTEL1	G_T	Imputed	Prost/ColR	0.117	1.2	1.11–1.23	1.3E-09	0.146	0.939	0.964	0.657	0.284
SQC	6p21.33	rs116822326	MHC	A_G	Imputed	Lung	0.155	1.3	1.19–1.32	3.8E-19	0.392	0.774	0.132	0.498	0.103
SQC	12p13.33	rs7953330	RAD52	G_C	Oncoarray	Lung	0.315	0.9	0.83–0.90	7.3E-13	0.800	0.463	0.019	3.3E-03	0.424
SQC	22q12.1	rs17879961	CHEK2	A_G	Oncoarray	Lung	0.005	0.4	0.32–0.52	5.7E-13	0.441	0.360	0.041	0.040	0.805

denote novel locus identified to GWAS significance by this study; a, reference_effect. Bolded p-values indicate significant associations with consistent direction as expected. Genome positions relative to GRCh37, EAF, effective allele frequency; OR, odds (log additive) ratio; 95%CI, 95% confidence interval. P-value, based on fixed-effect meta-analysis adjusted for age, sex and genetically derived ancestry; CPD, cigarette per day; FTND, Fagerstrӧm Test for Nicotine Dependence; FEV1, forced expiratory volume in 1 second; FVC, forced vital capacity.

Adeno, adenocarcinoma; SQC, squamous cell carcinoma.

^ˆ

marker had an acceptable, but not ideal concordance rate (see Supplementary Note)