For in silico replication, we also obtained association results for 35 SNPs from 14,064 individuals of European ancestry from five studies (Supplementary Table 1). The five study cohorts, each including 856 to 5,373 individuals, were genotyped using the Illumina HumanHap 550, 300 or Illumina Human CNV370 DUO (Supplementary Tables 2 and 3). To allow for meta-analysis across different marker sets and to improve coverage of the genome, we carried out imputation of polymorphic (minor allele frequency >1%) autosomal HapMap SNPs (Supplementary Note and Supplementary Table 3) using either MACH or IMPUTE with the HapMap CEU sample as a reference panel. We accounted for uncertainty in each genotype prediction in the analysis of imputed genotype data by using either the dosage information from MACH or the genotype probabilities from IMPUTE. Stage 1 and 2 results for FTO and MC4R are not presented directly in the main text but are shown for comparison in Supplementary Table 5 and Supplementary Figure 5 online.
