Table 3.

Assessments of IGF gene-level associations with risk of BE using BEACON GWAS data via application of (A) PCA and (B) MAGMA(A) PCA

	Gene	Gene name	Chr	SNPsa	PCsb	P c	FDR qd
1	GHR	Growth hormone receptor	5	39	3	0.0022	0.022
2	IGF1R	IGF1 receptor	15	131	8	0.078	0.39
3	IGF2	IGF2	11	25	3	0.16	0.46
4	IGFBP6	IGF binding protein 6	12	6	3	0.18	0.46
5	IGFBP3	IGF binding protein 3	7	5	3	0.24	0.48
6	IGFBP5	IGF binding protein 5	2	16	3	0.32	0.50
7	IGFBP1	IGF binding protein 1	7	6	3	0.35	0.50
8	IGFBP2	IGF binding protein 2	2	8	3	0.47	0.59
9	IGF1	IGF1	12	25	3	0.62	0.62
10	IGFALS	IGFBP acid labile subunit	16	4	3	0.62	0.62
(B) MAGMA
	Gene	Chr	SNPsa	Pe	FDR qd
1	GHR	5	39	0.00046	0.0056
2	IGF1R	15	130f	0.0090	0.054
3	IGFBP5	2	16	0.12	0.44
4	IGF2	11	25	0.21	0.44
5	IGFBP3	7	5	0.21	0.44
6	IGFBP4	17	3	0.23	0.44
7	IGFBP6	12	6	0.26	0.44
8	GH1	17	2	0.40	0.59
9	IGFALS	16	4	0.51	0.65
10	IGFBP1	7	6	0.54	0.65
11	IGFBP2	2	8	0.69	0.75
12	IGF1	12	25	0.77	0.77

^aNumber of SNPs per gene.

^bNumber of gene-level PCs included in the logistic regression model.

^cLikelihood ratio P value.

^dFalse discovery rate q value.

^eGene-level P value.

^fga012685 not included in 1000G Phase 3 EUR reference data.