To identify additional SNPs with independent BMI associations at the 97 established loci, we used genome-wide complex trait analysis (GCTA)19 to perform approximate joint and conditional association analysis20 using summary statistics from European sex-combined meta-analysis after removing family-based validation studies (TwinGene and QIMR). GCTA confirmed two signals at MC4R previously identified using exact conditional analyses5, and identified five loci with evidence of independent associations (Table 3): second signals near LINC01122, NLRC3-ADCY9, GPRC5B-GP2 and BDNF, and a third signal near MC4R (rs9944545, Fig. 1b). Joint conditional analyses at two genomic regions separated by >500 kb (the AGBL4-ELAVL4 regions on chr. 1, and the ATP2A1-SBK1 regions on chr. 16), indicate that these pairs of signals may not be independent owing to extended LD.
