Table 1.

Two genome-wide significant SNPs for lung cancer risk after combining stage 1 and 2

Locus	Genes	SNP (reference, effect)	Model	Stage	Controls	Cases	EAF in controlc	EAF in casesc	OR	95%CI	P	Phet
15q25.1	CHRNA5	rs2036527 (C,T)a	Overall	Stage1	3601	1736	0.212	0.255	1.33	(1.20–1.48)	1.03E-07
				Stage2	1062	762	0.222	0.282	1.28	(1.09–1.51)	2.92E-03
				Combinedb	4663	2498	0.214	0.263	1.32	(1.20–1.44)	1.30E-09	0.70432
			Adeno only	Stage1	3601	739	0.212	0.254	1.28	(1.12–1.47)	4.06E-04
				Stage2	1062	284	0.222	0.282	1.31	(1.05–1.64)	1.83E-02
				Combinedb	4663	1023	0.214	0.262	1.29	(1.15–1.45)	2.28E-05	0.87615
			Squamous only	Stage1	3601	399	0.212	0.237	1.25	(1.04–1.51)	1.91E-02
				Stage2	1062	176	0.222	0.259	1.24	(0.93–1.66)	1.36E-01
				Combinedb	4663	575	0.214	0.244	1.25	(1.07–1.46)	5.59E-03	0.96628
5p15.33	TERT	rs2853677 (T,C)	Overall	Stage1	3600	1736	0.277	0.320	1.26	(1.14–1.38)	4.28E-06
				Stage2	1137	851	0.261	0.321	1.35	(1.16–1.56)	1.15E-04
				Combinedb	4737	2587	0.273	0.320	1.28	(1.18–1.39)	2.80E-09	0.45653
			Adeno only	Stage1	3600	739	0.277	0.341	1.34	(1.18–1.52)	4.44E-06
				Stage2	1137	311	0.261	0.339	1.45	(1.17–1.78)	5.55E-04
				Combinedb	4737	1050	0.273	0.340	1.37	(1.23–1.53)	1.27E-08	0.55297
			Squamous only	Stage1	3600	400	0.277	0.278	1.04	(0.87–1.25)	6.34E-01
				Stage2	1137	192	0.261	0.276	1.11	(0.85–1.46)	4.44E-01
				Combinedb	4737	592	0.273	0.277	1.06	(0.92–1.23)	4.16E-01	0.69993

^aStudy design failed; rs2036527 was used as surrogate for the original top SNP rs55781567 in stage 1.

^bFor the combined stage, the odds ratio and p values were generated using a fixed-effects meta-analysis approach. Heterogeneity was assessed using p-values for Cochran’s Q statistic.

^cEffective allele frequency in controls or cases