For the purpose of fine-mapping and identifying additional SNPs with putative functional implication using linkage disequilibrium (LD), a subset of nine discovery studies (FN-BMD n=21,699; LS-BMD n=20,835) used 1KGP data (Release June/2010) to re-impute genotypes contained in the 55 autosomal BMD loci (see Supplementary note for details). In 13 of the 55 BMD loci (X-chromosome SNP not included) we identified markers in a surrounding 1 Mb region that were imputed from 1KGP, and that were more significant than the original HapMap signal (Supplementary Tables 10 and 11) highlighting the benefit of using a denser reference panel of markers. All HapMap markers in LD with variants with functional annotation and displaying higher significance in the 1KGP meta-analysis are shown on Supplementary Table 12. In 14 of the 56 discovered BMD loci a marker from the HapMap imputation was highly correlated (r2 >0.8) with at least one putative functional variant annotated in the 1KG reference. Three of the 14 BMD loci associated with fracture contained putative functional variants tagged by the top SNPs of the BMD meta-analysis. These included the known rs3736228
