25 with LS-BMD and 19 with both. The overlap reflects the correlation between the femoral neck and lumbar spine measurements (Pearson correlation = 0.53). Of these 82 loci, 59, 18 and 5 were prioritized from the analysis in the sex-combined, women and men sample sets, respectively (Supplementary Table 1). The meta-analysis was extended to include the evaluation of 76,253 X-chromosome imputed markers across 14 of the discovery GWAS including 31,801 participants (see Online Methods). Five X-chromosome loci were associated at P<5×10−5 four of which were derived from the sex-combined analysis and one from the analysis in men only (Supplementary Table 1). We further performed genome-wide conditional analyses in all sex-combined stage 1 studies. Each study repeated the GWAS analysis but additionally adjusted for 82 SNPs representing the autosomal loci associated at P<5×10−6 (see Online Methods). We then meta-analyzed these studies in the same way as for the primary GWA study meta-analysis. Nine loci showed at least two independent association signals arising from this conditional analysis (Supplementary Fig. 4 and Supplementary Table 2) suggesting that allelic heterogeneity is underlying BMD variation. We also assessed all possible pairwise interactions of the 82 SNPs, but none were significant after adjusting for the number
