Table 1.

Replication and meta-analysis of 55 top SNPs for squamous cell lung carcinoma in NCI, UK1 and Texas.

Gene	Min-Pa SNP	MAFb	Risk allele	NCI		Texas		UK1		Meta-analysis
				ORc	Pd	ORc	Pd	ORc	Pd	ORc (95% CI)e	Pf
HLA-B	rs2596574	0.06	G	1.89	2.12×10−7	1.06	0.75	1.05	0.74	1.36 (1.16–1.60)	1.38×10−4
CSMD1	rs1382249	0.14	A	1.41	3.60×10−6			1.03	0.77	1.26 (1.12–1.41)	9.68×10−5
CD14/IK/SRA1	rs7721577	0.23	A	1.29	9.74×10−6	1.02	0.89	1.03	0.71	1.17 (1.07–1.27)	3.18×10−4
SKIV2L/C4B/C2/CFB	rs406936	0.11	G	1.43	1.79×10−5	1.07	0.62	1.05	0.63	1.23 (1.10–1.38)	4.49×10−4
RAD52	rs6489769	0.38	A	1.23	3.18×10−5	1.22	0.036	1.15	0.04	1.20 (1.12–1.30)	6.48×10−7
PPARGC1A	rs16874276	0.07	G	1.45	1.53×10−4			1.05	0.72	1.29 (1.11–1.50)	1.16×10−3
PON2	rs10240398	0.43	A	1.19	2.95×10−4	0.83	0.043	1.11	0.14	1.11 (1.03–1.19)	4.47×10−3
CDH1	rs8061932	0.18	A	1.25	4.28×10−4			0.89	0.22	1.13 (1.02–1.25)	2.38×10−2
C5	rs7027797	0.10	A	1.35	5.93×10−4			1.06	0.57	1.22 (1.07–1.40)	2.62×10−3
EPHX2	rs11780471	0.07	G	1.43	6.49×10−4			1.14	0.39	1.33 (1.12–1.58)	9.84×10−4
ERAP1	rs18036	0.24	G	1.21	7.00×10−4	1.05	0.68			1.17 (1.06–1.29)	1.37×10−3
PSEN1	rs214260	0.14	A	1.25	7.08×10−4	1.05	0.67	1.08	0.37	1.16 (1.06–1.27)	1.74×10−3
PMS2	rs12112229	0.22	A	1.21	7.25×10−4			1.08	0.36	1.16 (1.06–1.27)	9.88×10−4
NOTCH4	rs479536	0.04	G	1.64	7.38×10−4	1.04	0.82	1.07	0.61	1.24 (1.04–1.47)	1.48×10−2
IL4R	rs3024536	0.14	G	1.27	7.74×10−4	1.10	0.45	1.07	0.49	1.18 (1.07–1.31)	1.62×10−3
TNFSF14	rs237554	0.15	G	1.26	9.31×10−4	0.92	0.53	1.31	0.10	1.21 (1.09–1.34)	4.64×10−4
PSORS1C1	rs3130977	0.31	G	1.18	1.00×10−3	1.13	0.20			1.17 (1.07–1.27)	4.38×10−4
NFKBIA	rs1012919	0.32	G	1.18	1.39×10−3	0.87	0.15	0.99	0.90	1.07 (0.99–1.15)	8.45×10−2
BARD1	rs6712055	0.29	G	1.17	1.47×10−3	1.06	0.54	1.04	0.64	1.12 (1.04–1.21)	3.20×10−3
DEFA5	rs4841831	0.35	A	1.17	1.68×10−3			0.97	0.68	1.10 (1.02–1.20)	1.78×10−2
NFKB1	rs4648022	0.09	G	1.33	2.02×10−3	1.34	0.10	1.18	0.19	1.29 (1.12–1.47)	2.80×10−4
NRIP1	rs10482862	0.13	G	1.23	2.03×10−3	0.84	0.19	0.99	0.95	1.10 (1.00–1.22)	5.95×10−2
IL12A	rs2243154	0.10	G	1.30	2.14×10−3	0.85	0.35	0.90	0.36	1.10 (0.97–1.25)	0.13
NOS2	rs3794764	0.23	G	1.20	2.25×10−3	1.16	0.18	0.95	0.56	1.12 (1.02–1.22)	1.30×10−2
GADD45B	rs3729535	0.09	A	1.29	2.28×10−3	0.90	0.55	0.80	0.07	1.08 (0.95–1.23)	0.22
CDKN1C	rs367035	0.41	G	1.16	2.35×10−3	1.03	0.77	0.90	0.16	1.07 (0.99–1.14)	8.10×10−2
BAT3	rs3130617	0.21	A	1.20	2.61×10−3	1.07	0.50	1.11	0.17	1.15 (1.06–1.25)	1.38×10−3
TLR4	rs913930	0.34	G	1.16	2.62×10−3	0.92	0.38	0.99	0.86	1.06 (0.99–1.14)	8.17×10−2
PTGER1	rs1042728	0.08	A	1.31	2.71×10−3	1.30	0.19	0.89	0.37	1.17 (1.02–1.34)	2.13×10−2
CDK6	rs445	0.10	A	1.25	3.08×10−3	0.90	0.46	0.91	0.42	1.10 (0.98–1.23)	0.11
MPO	rs2071409	0.17	A	1.21	3.30×10−3	0.83	0.14	0.92	0.32	1.04 (0.95–1.14)	0.36
TCERG1	rs2400219	0.21	G	1.19	3.88×10−3	0.95	0.62	0.91	0.29	1.07 (0.98–1.16)	0.16
EDN3	rs6128532	0.49	A	1.14	4.16×10−3	0.97	0.72	1.10	0.18	1.10 (1.03–1.18)	6.58×10−3
MDM2	rs1470383	0.15	G	1.20	4.51×10−3	1.10	0.48	1.01	0.96	1.13 (1.03–1.25)	1.23×10−2
SMAD1	rs1866179	0.42	A	1.14	4.78×10−3	1.12	0.22	0.95	0.47	1.09 (1.01–1.17)	2.31×10−2
CYP17A1	rs4919686	0.30	A	1.16	4.82×10−3			1.11	0.18	1.14 (1.05–1.24)	1.88×10−3
PTGDR	rs809722	0.19	A	1.18	5.10×10−3	1.05	0.67	1.03	0.73	1.12 (1.02–1.18)	1.30×10−2
APOA5	rs1263167	0.19	G	1.18	5.21×10−3	1.10	0.41	0.97	0.71	1.11 (1.01–1.21)	2.37×10−2
CMA1	rs4982958	0.38	G	1.14	5.24×10−3	0.96	0.66	1.08	0.25	1.10 (1.02–1.18)	1.13×10−2
CCR1	rs17283264	0.07	G	1.28	5.28×10−3			1.03	0.84	1.20 (1.04–1.38)	1.43×10−2
MIF	rs875643	0.43	G	1.14	5.86×10−3	0.98	0.86	0.91	0.21	1.05 (0.98–1.13)	0.19
B2M	rs1901531	0.20	A	1.18	6.14×10−3	1.02	0.89	1.00	1.00	1.14 (1.03–1.27)	1.48×10−2
IRAK1	rs1059702	0.14	A	1.13	6.78×10−3	1.06	0.73			1.13 (1.03–1.23)	7.04×10−3
BMP4	rs10873077	0.09	A	1.25	8.28×10−3			0.94	0.66	1.14 (1.00–1.31)	5.55×10−2
CYBA	rs899729	0.40	G	1.13	8.86×10−3	0.91	0.30	1.03	0.64	1.07 (0.99–1.15)	7.31×10−2
HLA-DQA1	rs3129763	0.26	A	1.15	8.89×10−3	0.99	0.89	1.18	0.05	1.13 (1.04–1.23)	2.79×10−3
CYSLTR1	rs320996	0.21	A	1.11	9.74×10−3	1.08	0.57			1.11 (1.03–1.20)	8.34×10−3
RSBN1/PHTF1	rs2797409	0.26	A	1.15	1.03×10−2	0.83	0.085	1.18	0.05	1.10 (1.01–1.19)	2.38×10−2
IL20	rs1770372	0.09	A	1.24	1.09×10−2	0.97	0.86	0.92	0.49	1.10 (0.97–1.25)	0.13
PSMD9	rs895959	0.15	A	1.18	1.25×10−2	0.93	0.56	0.93	0.51	1.07 (0.97–1.19)	0.16
HLA-A	rs1655900	0.13	A	1.19	1.27×10−2	1.08	0.56	1.11	0.23	1.15 (1.04–1.26)	6.04×10−3
SLC23A1	rs10900862	0.35	G	1.13	1.56×10−2	1.00	0.97	1.15	0.06	1.11 (1.03–1.20)	4.75×10−3
MUC1	rs4971100	0.41	A	1.12	1.57×10−2	0.92	0.37	1.11	0.14	1.09 (1.01–1.16)	2.26×10−2
FANCD2	rs7615646	0.15	G	1.17	1.58×10−2			0.88	0.16	1.07 (0.96–1.18)	0.30
TNMD	rs5966709	0.36	G	1.09	2.28×10−2	0.98	0.88			1.08 (1.01–1.15)	3.37×10−2

^aThe SNP with the smallest P-value of association with cancer risk mapping to the gene.

^bMinor allele frequency in the NCI controls.

^cOdds ratio.

^dTwo-sided P-value.

^e95% confidence interval.

^fMeta-analysis two-sided P-value based on a fixed effect model.