Table 4 Replication of C11orf30/LRRC32 (rs2212434) and the clade B serpins gene cluster (rs12964116 and rs1243064) in the Chicago Food Allergy Study

SNP ID	EA/AA	Trait	GOFA discovery set			GOFA replication set			Chicago Food Allergy Study			Meta-analysis
			AF_cases	AF_controls	P value	AF_cases	AF_controls	P value	AF_cases	AF_controls ^a	P value	P value
rs2212434	T/C	FA	0.511	0.448	3.4 × 10⁻⁴	0.540	0.451	8.2 × 10⁻⁵	0.512	0.469	1.4 × 10⁻⁴	9.2 × 10⁻¹¹
		HE	0.528	0.448	2.3 × 10⁻⁴	0.525	0.451	0.012	0.492	0.471	0.24	1.3 × 10⁻⁵
		PN	0.505	0.448	0.020	0.550	0.451	4.2 × 10⁻³	0.497	0.471	0.12	2.3 × 10⁻⁴
		CM	0.530	0.448	3.3 × 10⁻³	0.530	0.451	0.039	0.514	0.469	9.8 × 10⁻³	1.3 × 10⁻⁵
rs12964116	G/A	FA	0.080	0.043	5.7 × 10⁻⁶	0.069	0.044	9.4 × 10⁻³	0.061	0.050	0.010	1.8 × 10⁻⁸
		HE	0.063	0.043	0.32	0.070	0.044	0.019	0.065	0.052	0.14	6.0 × 10⁻⁴
		PN	0.095	0.043	1.2 × 10⁻⁶	0.058	0.044	0.35	0.084	0.050	5.8 × 10⁻⁶	1.9 × 10⁻¹⁰
		CM	0.077	0.043	2.2 × 10⁻³	0.061	0.044	0.18	0.041	0.051	0.29	0.11
rs1243064	A/T	FA	0.322	0.246	4.3 × 10⁻⁷	0.278	0.244	0.20	0.265	0.264	0.56	5.1 × 10⁻⁵
		HE	0.343	0.246	1.6 × 10⁻⁷	0.306	0.244	0.028	0.288	0.262	0.15	8.0 × 10⁻⁸
		PN	0.325	0.246	4.6 × 10⁻⁵	0.267	0.244	0.38	0.279	0.264	0.20	2.2 × 10⁻⁴
		CM	0.358	0.246	9.8 × 10⁻⁷	0.280	0.244	0.36	0.244	0.261	0.31	0.013

AA alternative allele, AF effect allele frequency, CM cow’s milk, EA effect allele, FA food allergy, GOFA Genetics of Food Allergy Study, HE hen’s egg, PN peanut
^a Controls of the Chicago Food Allergy Study include unaffected controls (n = 144) and controls of unknown phenotype (n = 1382). The AFs in both groups are presented in Supplementary Table 4

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