Head-and-neck squamous cell carcinoma risk in smokers: no association detected between phenotype and AHR, CYP1A1, CYP1A2, or CYP1B1 genotype

Jorge-Nebert, Lucia F.; Zhang, Ge; Wilson, Keith M.; Jiang, Zhengwen; Butler, Randall; Gluckman, Jack L.; Pinney, Susan M.; Nebert, Daniel W.

doi:10.1186/s40246-016-0094-y

Human Genomics

Table 3 Comparison of allele frequencies (additive model), as tested by chi-square analysis and permutations test, of individual tag-SNPs, HS vs. HR samples, entire cohort (N = 211)

From: Head-and-neck squamous cell carcinoma risk in smokers: no association detected between phenotype and AHR, CYP1A1, CYP1A2, or CYP1B1 genotype

Gene	Tag-SNP #	SNP ID	Asso-ciated allele^a	Cases (HS) allele frequencies	Controls (HR) allele frequencies	P value (chi-square analysis)	P value, following 100 K permutations
AHR	1	rs62444550	A	0.433	0.419	0.7741	1.00
AHR	2	rs77821156	A	0.929	0.889	0.1553	0.7627
AHR	3	rs10250822	C	0.272	0.197	0.0693	0.4745
AHR	4	rs4719497	C	0.174	0.096	0.0200^*	0.1727
AHR	5	rs3757824	T	0.862	0.793	0.0613	0.4203
AHR	7	rs713150	G	0.263	0.197	0.1068	0.6212
AHR	8	rs17722841	G	0.817	0.798	0.6212	0.9998
AHR	9	rs2282885	A	0.665	0.591	0.1147	0.6360
AHR	10	rs2282883	T	0.397	0.343	0.2531	0.9128
AHR	11	rs4236290	T	0.902	0.874	0.3607	0.9774
AHR	12	rs2158041	T	0.250	0.212	0.3578	0.9742
AHR	13	rs3802082	A	0.884	0.838	0.1751	0.8056
AHR	14	rs7811989	A	0.295	0.253	0.3335	0.9620
AHR	15	rs2074113	G	0.942	0.914	0.2670	0.9201
AHR	16	rs2066853	A	0.107	0.091	0.5783	0.9996
CYP1A1	1	rs4646903	G	0.125	0.086	0.1936	0.7207
CYP1A1	2	rs2606345	C	0.397	0.354	0.3543	0.9355
CYP1A1	3	rs3826042	C	0.960	0.939	0.3355	0.9121
CYP1A1	4	rs7495708	C	0.205	0.177	0.4567	0.9711
CYP1A2	1	rs2069514	A	0.089	0.030	0.0119 ^*	0.0896
CYP1A2	2	rs762551	A	0.723	0.717	0.8902	1.0000
CYP1A2	3	rs2470890	C	0.438	0.354	0.0787	0.4071
CYP1A2	4	rs17861162	G	0.076	0.040	0.1233	0.5885
CYP1B1	1	rs162562	G	0.317	0.217	0.0212 ^*	0.1262
CYP1B1	2	rs1800440	T	0.862	0.818	0.2232	0.7441
CYP1B1	3	rs1056837	A	0.478	0.460	0.7103	0.9998
CYP1B1	4	rs1056836	C	0.482	0.460	0.6433	0.9979
CYP1B1	5	rs1056827	A	0.317	0.273	0.3206	0.8683
CYP1B1	6	rs10012	C	0.326	0.268	0.1922	0.6692
CYP1B1	7	rs162558	T	0.821	0.758	0.1071	0.4914
CYP1B1	8	rs2855655	C	0.562	0.551	0.8045	1.0000
CYP1B1	9	rs162557	A	0.272	0.232	0.3459	0.9051
CYP1B1	10	rs162556	A	0.567	0.525	0.3903	0.9346
CYP1B1	11	rs162555	T	0.826	0.768	0.1367	0.5529
CYP1B1	12	rs10175368	C	0.746	0.742	0.9417	1.0000

^*Statistically significant (P < 0.05)
^aAssociated allele, as selected by the HaploView program

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ISSN: 1479-7364

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