The targeted 16q12.2/FTO fine-mapping region spans 646 kb from 53,539,509 to 54,185,773 (build 37) on the long arm of chromosome 16 (16q12.2), including the large FTO gene (411 kb) as well as 198 kb downstream of FTO, which includes the RPGRIP1L gene and 37 kb upstream of FTO (Figure 1). On average, we successfully genotyped or imputed one SNP per 172 bp ( = 646,264 bp/3,756 SNPs). The allele frequency distribution of the 3,756 SNPs in this region is shown in Table 2. In contrast to GWAS platforms, a large fraction of SNPs have allele frequencies <5% (52.5%), including 16.7% with allele frequency <1%. Twenty-one SNPs are within the exons of FTO and RPGRIP1L, of which 7 are synonymous and 14 are missense (2 synonymous and 4 missense are located in FTO).
