We used data from the 1000 Genomes Project and the HapMap Consortium to explore whether the 32 confirmed BMI SNPs were in LD (r2 ≥ 0.75) with common missense SNPs or copy number variants (CNVs) (Online Methods). Non-synonymous variants in LD with our signals were present in the BDNF, SLC39A8, FLJ35779/HMGCR, QPCTL/GIPR, MTCH2, ADCY3, and LBXCOR1 genes. In addition, the rs7359397 signal was in LD with coding variants in several genes including SH2B1, ATNX2L, APOB48R, SULT1A2, and AC138894.2 (Table 1, Fig. 3, Supplementary Table 6 and Supplementary Fig. 2). Furthermore, two SNPs tagged common CNVs. The first CNV was previously identified and is a 45-kb deletion near NEGR19. The second CNV is a 21-kb deletion that lies 50kb upstream of GPRC5B; the deletion allele is tagged by the T-allele of rs12444979 (r2 = 1) (Fig. 3). Although the correlations with potentially functional variants does not prove that these variants are indeed causal, these provide first clues as to which genes and variants at these loci might be prioritized for fine-mapping and functional follow-up.
