BMI SNPs were catalogued from a BMI meta-analyses by Speliotes and colleagues [9]. The meta-analyses identified 32 SNPs reaching genome-wide significance (p < 5x10−8) (Additional file 1: Table S1). The SAGE sample was not included in the meta-analysis and represents and independent sample to test BMI loci. Fifteen SNPs did not appear on the genotyping array. Ungenotyped markers were ascertained by two approaches in order to compare methods: 1) imputation and 2) proxy SNPs. Imputed SNPs analyzed had allele frequency greater than 1% (Additional file 1: Table S1) and imputation quality greater than 0.8. The proxy method used the LD structure of the genome to identify highly correlated SNPs that appear on the array as substitutes for the unobserved SNPs. Proxy SNPs were identified using SNP Annotation and Proxy Search V2.1 [41] using the HapMap release 22 CEU reference panel except for rs11847697, which did not have a highly correlated SNP (r2 < 0.7) and was therefore not included in SNP-GRSSs. Proxy SNP information appears in Additional file 1: Table S1b. BMI and obesity associated CNVs were catalogued from research
