SNPs were included as part of the Metabochip, a 200 k Illumina customized iSelect array developed through the collaborative efforts of several consortia working on metabolic syndrome related diseases. Details on the design can be found elsewhere (http://www.sph.umich.edu/csg/kang/MetaboChip/). In brief, SNPs within the 16q12.2/FTO region were selected based on 1000 Genomes Pilot 1 and HapMap phase 2. The boundaries around each GWAS index SNP were determined by identifying all SNPs with r2≥0.5 with the index SNP, and then expanding the initial boundaries by 0.02 cM in either direction using the HapMap-based genetic map [46]. The total interval size of the 16q12.2/FTO region was 646 kb. All 1000 Genomes Pilot 1 SNPs obtained from Sanger Institute (August 12, 2009) and the Broad Institute (August 11, 2009) were considered as potential fine mapping SNPs, unless SNP allele frequency was <0.01 in all three HapMap samples (CEU, YRI and HBC/JPT). SNPs were excluded if (a) the Illumina design score was <0.5 or (b) there were SNPs within 15 bp in both directions of the SNP of interest with allele frequency of >0.02 among
