After replication, the conditional analysis provided significant evidence of association (P<5×10−8) in 8 of the 9 loci containing secondary signals (Supplementary Fig. 4 and Supplementary Table 2). Three loci included variants localized less than 40 Kb from the initial main signal suggesting allelic heterogeneity and included the 1p31.3 (represented by rs17482952 near WLS), 6q25.1 (rs7751941 near ESR1) and the 16q12.1 (rs1564981 near CYLD) loci. The secondary signal in 16q12.1 (rs1564981) showed a strong association with LS-BMD, while the main signal in this locus (rs1566045) was only associated with FN-BMD. The other five secondary signals were represented by variants localized at more than 180kb away from the initial main signal and contained different candidate genes including the 1p36.12 (rs7521902 near WNT4), 7p14.1 (rs10226308 near SFRP4), 7q31.31 (rs13245690 near C7orf58), 12q13.13 (rs736825 near HOXC6) and the 17q21.31 (rs4792909 near SOST) loci. The secondary signal mapping to the 13q14.11 locus (rs7326472) did not achieve genome-wide significance after replication.
