Asthma and genes encoding components of the vitamin D pathway

Bossé, Yohan; Lemire, Mathieu; Poon, Audrey H; Daley, Denise; He, Jian-Qing; Sandford, Andrew; White, John H; James, Alan L; Musk, William Arthur; Palmer, Lyle J; Raby, Benjamin A; Weiss, Scott T; Kozyrskyj, Anita L; Becker, Allan; Hudson, Thomas J; Laprise, Catherine

doi:10.1186/1465-9921-10-98

Respiratory Research

Table 3 Single SNP association results for asthma and atopy in the replication samples.

From: Asthma and genes encoding components of the vitamin D pathway

			Asthma												Atopy
			SAGE				CAPPS				BHS				SAGE				CAPPS				BHS
Genes	SNPs	Allele	AF	Fa	Z	p	AF	Fa	Z	p	AF case	AF ctrl	X ²	p	AF	Fa	Z	p	AF	Fa	Z	p	AF case	AF ctrl	X ²	p
IL10	rs4844553	A	0.07	25	0.96	0.336	0.05	11	0.3	0.763	0.05	0.06	1.21	0.272	0.07	35	-0.16	0.873	0.05	22	-1.88	0.061	0.05	0.06	0.12	0.729
		G	0.93	25	-0.96	0.336	0.95	11	-0.3	0.763					0.93	35	0.16	0.873	0.95	22	1.88	0.061
	rs3024498	A	0.78	83	3.06	0.002	0.78	40	-2.56	0.01	0.70	0.72	1.74	0.187	0.78	108	1.22	0.223	0.78	70	-0.54	0.592	0.71	0.72	0.26	0.608
		G	0.23	83	-3.06	0.002	0.22	40	2.56	0.01					0.23	108	-1.22	0.223	0.22	70	0.54	0.592
	rs3024492	A	0.78	81	2.89	0.004	0.78	40	-2.56	0.01	0.70	0.72	1.55	0.213	0.78	108	1.13	0.26	0.78	69	-0.75	0.453	0.71	0.72	0.20	0.655
		T	0.22	81	-2.89	0.004	0.22	40	2.56	0.01					0.22	108	-1.13	0.26	0.22	69	0.75	0.453
	rs3024490	A	0.28	69	0.63	0.527	0.29	34	-1.64	0.101	0.24	0.22	1.63	0.202	0.28	99	0.36	0.717	0.29	78	0	1	0.23	0.23	0.07	0.788
		C	0.72	69	-0.63	0.527	0.71	34	1.64	0.101					0.72	99	-0.36	0.717	0.71	78	0	1
	rs1800872	A	0.28	70	0.73	0.463	0.3	34	-1.64	0.101	0.24	0.22	1.64	0.200	0.28	98	0.46	0.649	0.3	78	-0.1	0.922	0.23	0.23	0.07	0.786
		C	0.72	70	-0.73	0.463	0.7	34	1.64	0.101					0.72	98	-0.46	0.649	0.7	78	0.1	0.922
	rs1800896	C	0.43	87	-1.22	0.221	0.43	40	2.29	0.022	0.50	0.50	0.02	0.889	0.43	124	-0.55	0.583	0.43	83	0.29	0.772	0.50	0.50	0.06	0.804
		T	0.57	87	1.22	0.221	0.58	40	-2.29	0.022					0.57	124	0.55	0.583	0.58	83	-0.29	0.772
	rs10494879	C	0.63	93	1.44	0.151	0.64	42	-2.07	0.039	0.55	0.56	0.51	0.476	0.63	127	0.08	0.938	0.64	82	-1.18	0.239	0.55	0.56	0.13	0.717
		G	0.37	93	-1.44	0.151	0.36	42	2.07	0.039					0.37	127	-0.08	0.938	0.36	82	1.18	0.239
IL1RL1	rs1420089	C	0.09	39	1.41	0.16	0.09	19	-0.23	0.819	0.11	0.11	0.08	0.782	0.09	50	1.91	0.057	0.09	40	0	1	0.12	0.12	0.03	0.874
		T	0.91	39	-1.41	0.16	0.91	19	0.23	0.819					0.91	50	-1.91	0.057	0.91	40	0	1
	rs1041973	A	0.22	80	-0.1	0.921	0.23	35	0.16	0.876					0.22	98	-1.99	0.046	0.23	73	0.11	0.915
		C	0.78	80	0.1	0.921	0.77	35	-0.16	0.876					0.78	98	1.99	0.046	0.77	73	-0.11	0.915
	rs1946131	A	0.11	43	-0.3	0.768	0.1	16	-0.23	0.819	0.10	0.10	0.36	0.55	0.11	52	-1.05	0.294	0.1	37	0.78	0.435	0.10	0.09	1.61	0.205
		G	0.9	43	0.3	0.768	0.9	16	0.23	0.819					0.9	52	1.05	0.294	0.9	37	-0.78	0.435
CD86	rs9282641	C	0.93	36	0.8	0.423	0.93	14	-0.78	0.439	0.89	0.92	7.34	0.007	0.93	42	0	1	0.93	35	-0.16	0.873	0.91	0.90	0.82	0.365
		T	0.07	36	-0.8	0.423	0.07	14	0.78	0.439					0.07	42	0	1	0.07	35	0.16	0.873
	rs9831894	G	0.42	88	-1.12	0.261	0.4	40	-2.61	0.009	0.39	0.39	0.00	0.952	0.42	124	-0.23	0.817	0.4	96	-0.26	0.792	0.39	0.40	0.21	0.645
		T	0.58	88	1.12	0.261	0.6	40	2.61	0.009					0.58	124	0.23	0.817	0.6	96	0.26	0.792
	rs2332096	G	0.57	87	-1.53	0.127	0.56	43	-2.36	0.018	0.53	0.55	0.47	0.491	0.57	129	-1.08	0.28	0.56	94	-0.92	0.357	0.54	0.54	0.00	0.958
		T	0.44	87	1.53	0.127	0.44	43	2.36	0.018					0.44	129	1.08	0.28	0.44	94	0.92	0.357
CYP2R1	rs11023374	C	0.27	72	-0.63	0.532	0.27	35	0.44	0.662	0.27	0.28	0.07	0.793	0.27	91	0.38	0.703	0.27	72	1.05	0.292	0.28	0.27	0.08	0.775
		T	0.73	72	0.63	0.532	0.73	35	-0.44	0.662					0.73	91	-0.38	0.703	0.73	72	-1.05	0.292
	rs10500804	G	0.4	92	1.81	0.07	0.44	40	-0.41	0.68	0.41	0.44	4.25	0.039	0.4	119	0.72	0.47	0.44	94	0.81	0.421	0.42	0.43	0.30	0.582
		T	0.6	92	-1.81	0.07	0.56	40	0.41	0.68					0.6	119	-0.72	0.47	0.56	94	-0.81	0.421
	rs1562902	C	0.46	93	-0.83	0.405	0.42	39	-0.42	0.674	0.47	0.43	4.71	0.03	0.46	126	0.16	0.874	0.42	93	-0.62	0.538	0.46	0.43	2.38	0.123
		T	0.54	93	0.83	0.405	0.58	39	0.42	0.674					0.54	126	-0.16	0.874	0.58	93	0.62	0.538
CYP24A1	rs8124792	A	0.06	30	0.17	0.862	0.08	12	-0.26	0.796	0.06	0.06	0.29	0.591	0.06	42	1.18	0.238	0.08	40	0.15	0.881	0.07	0.05	4.65	0.031
		G	0.94	30	-0.17	0.862	0.93	12	0.26	0.796					0.94	42	-1.18	0.238	0.93	40	-0.15	0.881
	rs927650	C	0.54	94	0.81	0.417	0.57	41	-0.69	0.492	0.55	0.50	6.75	0.009	0.54	127	0.23	0.816	0.57	100	0.78	0.439	0.54	0.52	0.89	0.344
		T	0.46	94	-0.81	0.417	0.43	41	0.69	0.492					0.46	127	-0.23	0.816	0.43	100	-0.78	0.439
	rs912505	A	0.75	75	0.53	0.596	0.73	29	0.69	0.493	0.78	0.79	0.41	0.521	0.75	106	0.83	0.409	0.73	86	-0.2	0.843	0.77	0.79	1.64	0.200
		G	0.25	75	-0.53	0.596	0.27	29	-0.69	0.493					0.25	106	-0.83	0.409	0.27	86	0.2	0.843
	rs2248359	A	0.35	87	1.04	0.296	0.44	41	1.82	0.069	0.41	0.41	0.02	0.889	0.35	133	0.54	0.588	0.44	97	2.51	0.012	0.42	0.40	1.14	0.287
		G	0.65	87	-1.04	0.296	0.56	41	-1.82	0.069					0.65	133	-0.54	0.588	0.56	97	-2.51	0.012
	rs2426498	C	0.87	49	-1.39	0.166	0.87	24	0.82	0.414	0.86	0.87	0.03	0.859	0.87	58	-2.14	0.032	0.87	61	0.25	0.806	0.86	0.87	0.06	0.814
		G	0.13	49	1.39	0.166	0.13	24	-0.82	0.414					0.13	58	2.14	0.032	0.13	61	-0.25	0.806
	rs6068821	A	0.41	95	2.32	0.021	0.45	39	0.27	0.785	0.41	0.39	1.15	0.283	0.41	126	2.24	0.025	0.45	96	1.17	0.241	0.42	0.40	1.07	0.302
		G	0.59	95	-2.32	0.021	0.55	39	-0.27	0.785					0.59	126	-2.24	0.025	0.55	96	-1.17	0.241

CAPPS, Canadian Asthma Primary Prevention Study; SAGE, Study of Asthma Genes and the Environment; BHS, Busselton Health Study; AF, allele frequency; Fa, Number of informative families to conduct the test.
P values below 0.05 are shown in bold. SNPs that are significant in the SLSJ study (Table 2) are underlined as well as the allele that increases the risk in that study. Coding non-synonymous SNPs are shown in bold.

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