a, Overall study design. b, From top to bottom, quantile–quantile plots for the sex‐combined single SNV meta‐analysis, sex‐stratified single SNV meta‐analysis (forearm phenotype consists solely of female‐only cohorts), and sex‐combined single SNV conditional meta‐analysis Plots depicts P values prior (blue) and after (red) conditional analysis on genome-wide significant variants (see Supplementary Methods). c, From top to bottom, Manhattan plots for sex‐combined meta‐analysis for lumbar spine BMD, femoral neck BMD, and forearm BMD. Each plot depicts variants from the UK10K/1000G reference panel with MAF > 0.5% across the 22 autosomes (odd, grey; even, black) against the −log10 P value from the meta‐analysis of 7 cohorts (dots). Also depicted are the subset variants from the reference panel that are also present in ref. 8 with P value <5 × 10−6 (diamonds). Variants with MAF < 5% and P < 1.2 × 10−6 are also depicted (red). d, Quantile–quantile plots for the sex‐combined meta‐analysis of lumbar spine, femoral neck, and forearm BMD for SNVs present across both exome‐sequenced and genome-sequenced and imputed cohorts, that is, SNV present only in genome-sequenced or imputed cohorts are not shown. e, Manhattan plot for the meta‐analysis of sex‐combined results for lumbar spine BMD for SNVs present in exome‐sequenced and genome-sequenced and imputed cohorts, that is, SNV present only in genome-sequenced or imputed cohorts are not shown (from left to right: lumbar spine, forearm and femoral neck BMD).