SMR tests identified two genes (ASB16-AS1 and TMUB2) that were significantly associated with FN-BMD, two genes (SYN2 and LRP3) were associated with LS-BMD and no genes were identified to be associated with FA-BMD (Table 1). Of the four genes, only ASB16-AS1 and SYN2 passed HEIDI tests (PHEIDI > 0.05), suggesting that there was no heterogeneity and gene expression of ASB16-AS1 (or SYN2) and the BMD variation were affected by the same variant. Using the GAGE eQTL data, we re-conducted the SMR tests. ASB16-AS1 was successfully verified to be associated with FN-BMD with PSMR = 1.98 × 10−8 and PHEIDI = 0.13. SYN2 was successfully verified to be associated with LS-BMD with PSMR = 2.51 × 10−5 and PHEIDI = 0.31. In the cis-eQTL region of SYN2 probe, there was no SNP with a GWAS p value < 5 × 10−8 (Fig. 1B). Therefore, SYN2 was a new gene associated with BMD discovered by the SMR test. The details of the results were shown in Table 1. The genes TMUB2 and LRP3 failed to pass the HEIDI tests suggesting there were
