Table 2.

The Association between Sentinel Variants Representing Each Lung Cancer Locus and Lung Cancer Risk

Category	Stratum	Locus	SNV*	Allele†	rsID	Gene	Type	EAF (Case/Control)‡	HGVSp	OR (95% CI)§	P Value§
Novel	LC	2p13.1	2:74046345:A:G	A/G	rs202197044	TET3	Missense	0.0010/0.00018	p.His143Arg	154.1 (26.8–883.9)	3.60 × 10−8
Novel	LC	7q31.33	7:124858989:C:T	C/T	rs202187871	POT1	Missense	0.0011/0.00022	p.Asp224Asn	10.60 (4.63–24.22)	2.21 × 10−8
Novel	LC	5q31.2	5:139481561:C:G	C/G	rs7447927	TMEM173	Synonymous	0.723/0.741	p.Val48Val	0.93 (0.91–0.95)	1.32 × 10−9
Novel	Smoker	20p13	20:3545768:C:T	C/T	rs140624366	ATRN	Synonymous	0.00029/0.000024	p.Leu205Leu	9.28 (2.80–30.72)	2.97 × 10−9
Known	LC	5p15.33	5:1293971:C:T	C/T	rs2736098	TERT	Synonymous	0.305/0.277	p.Ala305Ala	1.13 (1.10–1.16)	6.67 × 10−16
Known	Smoker	6p21.32	6:32293475:T:G	G/A	rs7775397	MHC	Missense	0.141/0.129	p.Lys400Gln	1.15 (1.11–1.19)	1.01 × 10−8
Known	LC	15q25.1	15:78590583:G:A	G/A	rs16969968	CHRNA5	Missense	0.373/0.330	p.Asp398Asn	1.25 (1.24–1.27)	2.00 × 10−54
Known	LC	19q13.2	19:40844710:G:A	G/A	rs28399462	CYP2A6	Synonymous	0.015/0.023	p.Pro408Pro	0.77 (0.71–0.83)	2.99 × 10−10

Definition of abbreviations: CI = confidence interval; EAF = effect allele frequency; HGVSp = Human Genome Variation Society protein nomenclature; LC = overall lung cancer; OR = odds ratio; rsID = reference SNP ID number; SNVsingle-nucleotide variant.

^*Genome position was based on GRCh38 (Genome Reference Consortium human build 38) coordinate.

^† Reference allele/effect allele.

^‡ We report the EAF using the discovery set (UK Biobank Whole-Exome Sequencing Project).

^§ The ORs and P values were calculated from the meta-analysis of the discovery and replication sets.