To identify global enrichment of data sets at the BMI-associated loci we performed permutation-based tests in a subset of 41 open chromatin (DNase-seq), histone modification (H3K27ac, H3K4me1, H3K4me3 and H3K9ac), and transcription factor binding data sets from the ENCODE Consortium22, Roadmap Epigenomics Project23 and when available the ENCODE Integrative Analysis60,72 (Supplementary Table 19). We processed Roadmap Epigenomics sequencing data with multiple biological replicates using MACS2 (ref. 73) and then applied same Irreproducible Discovery Rate pipeline used in the ENCODE Integrative Analysis60,72. Roadmap Epigenomics data with only a single replicate were analysed using MACS2 alone. We examined variants in LD with 97 BMI index SNPs based on r2 > 0.7 from the 1000 Genomes phase 1 version 2 EUR samples74. We matched the index SNP at each locus with 500 variants having no evidence of association (P > 0.5, ~1.2 million total variants) with a similar distance to the nearest gene (± 11,655 bp), number of variants in LD (±8 variants), and minor allele frequency. Using these pools, we created 10,000 sets of control variants for each of the 97 loci
