Table 2 Principal phenotype

	Gene	SNP	Cases			Controls			Genotype association		Allele association
			Total	% failed	Freq	Total	% failed	Freq	χ² 2df	χ² p Value	Odds ratio	χ² 1df	χ² p Value
A	GMCSF	rs7727544	415	5.80	0.40	576	13.0	0.45	6.56	0.038	0.83 (0.69–1.01)	3.61	0.058
	SLC22A5	rs274549	415	2.70	0.18	576	2.6	0.13	8.20	0.017	1.39 (1.08–1.79)	6.43	0.011
	SLC22A5	rs14701	415	1.4	0.18	576	3.6	0.13	11.69	0.003	1.46 (1.13–1.87)	8.32	0.004
	IL13	rs1800925	415	1.9	0.18	576	4.9	0.21	2.14	0.343	0.85 (0.67–1.07)	1.79	0.181
	IL13	rs1295686	415	1.4	0.19	576	2.6	0.18	0.48	0.788	1.08 (0.86–1.36)	0.37	0.544
	IL13	rs20541	415	0.2	0.18	576	6.8	0.15	3.46	0.177	1.25 (0.98–1.59)	3.04	0.081
	CNS-1	rs2243302	415	1.45	0.11	576	2.78	0.13	2.39	0.303	0.8 (0.61–1.06)	2.19	0.139
	IL4	rs2243250	415	4.8	0.14	576	5.2	0.11	5.99	0.050	1.30 (0.99–1.71)	3.36	0.067
	IL4	rs2070874	415	3.6	0.15	576	6.8	0.12	8.87	0.012	1.32 (1.01–1.72)	3.87	0.049
	IL4	rs734244	415	5.1	0.15	576	5.2	0.12	6.34	0.042	1.31 (1.00–1.72)	3.62	0.057
	IL4	rs2227284	415	3.9	0.27	576	8.2	0.22	5.09	0.078	1.27 (1.03–1.58)	4.85	0.028
	IL4	rs2243268	413	1.0	0.15	576	2.1	0.12	3.27	0.195	1.26 (0.97–1.64)	2.82	0.093
	IL4	rs2243270	415	3.4	0.16	576	4.7	0.13	7.55	0.023	1.34 (1.03–1.73)	4.58	0.032

B	SLC22A5	rs14701	780	3.1	0.17	1045	3.6	0.14	7.52	0.023	1.21 (1.01–1.45)	3.91	0.048
	IL13	rs1800925	780	1.9	0.18	1045	3.4	0.19	0.45	0.800	0.96 (0.81–1.14)	0.19	0.665
	IL13	rs1295686	780	1.2	0.20	1045	1.9	0.18	3.00	0.223	1.15 (0.97–1.36)	2.59	0.108
	IL13	rs20541	782	3.6	0.19	1045	6.1	0.16	5.14	0.077	1.23 (1.03–1.46)	4.92	0.027
	IL4	rs2243250	780	3.3	0.15	1044	3.9	0.13	4.42	0.110	1.22 (1.00–1.48)	3.75	0.053
	IL4	rs2070874	779	3.0	0.15	1045	4.2	0.13	3.95	0.139	1.18 (0.98–1.43)	2.83	0.092
	IL4	rs2243270	780	5.1	0.16	1045	4.7	0.14	3.58	0.167	1.18 (0.97–1.42)	2.69	0.101

Single SNP association statistics for all SNPs with positive findings and those used in haplotype analysis: (A) Cohort 1. (B) Total cohort. Association statistics for all 48 htSNPs genotyped in cohort 1 are available in table 2A in the online supplement.
Freq, frequency.