0E−06 39.7 0.011 rs2016266 0.003  12 SP1 7 52060245 52096493 64.8 8.0E−06 rs10876432 1.0E−06 26.0 0.011 rs2016266 0.003  12 AAAS 8 51987506 52001679 116.3 9.0E−06 rs10876432 1.0E−06 39.7 0.012 rs2016266 0.003  9 CDK5RAP2 16 122190967 122382258 99.0 9.0E−06 rs3780674 7.1E−06 41.2 0.016 rs3780674 0.001  12

PFDN5 8 51975501 51979501 116.3 1.5E−05 rs10876432 1.0E−06 MI-503 chemical structure 39.7 0.011 rs2016266 0.003  6 ESR1 61 152053323 152466101 234.0 2.7E−05 rs2504063 5.6E−08 176.9 6.0E−04 rs3020331 8.0E−06  12 MFSD5 11 51932146 51934455 73.1 8.8E−05 rs7314769 8.8E−05 26.6 0.046 rs2272313 0.030  12 RARG 12 51890619 51912303 71.7 1.2E−04 rs7314769 8.8E−05 30.6 0.031 rs2272300 0.014 Table 3 Genes associated at gene-based genome-wide significant and suggestive level with femoral neck BMD in dCG study (n = 5,858) Gene information Lumbar spine BMD Femoral neck BMD Chr Gene Number of SNPs Start position End position Test statistic Gene-based p Best SNP SNP p Test statistic Gene-based p Best SNP SNP p Significant gene  6 C6orf97 41 151856919 151984021 248.9 1.0E−06 rs4870044 4.0E−06 270.1 2.0E−06 rs7752591 2.2E−06  11 LRP4 12 46834993 46896652 32.7 0.040 rs7108147 0.004 126.5 4.0E−06 rs1007738 7.1E−06 Suggestive gene  11 CKAP5 12 46721659 46824419 28.2 0.079 rs7108147

0.004 144.9 1.1E−05 rs1007738 7.1E−06  20 ADRA1D 23 4149277 4177659 50.9 0.025 rs6076639 0.010 108.7 2.9E−05 rs4815683 1.6E−04  11 F2 7 46697318 46717632 8.8 0.282 rs4752926 0.063 80.7 3.4E−05 rs6485690 6.4E−05  1 KPRP 7 150997129 151001153 14.2 0.124 rs1332498 0.063 85.3 3.6E−05 rs1332498 3.3E−05

Tigecycline cell line Phosphoglycerate kinase  9 FOXE1 9 99655357 99658818 1.0 0.970 rs6586 0.529 84.7 6.5E−05 rs907580 4.6E−06  1 LCE4A 6 150948146 150948534 13.5 0.119 rs1332498 0.063 79.5 8.9E−05 rs1332498 3.3E−05  1 LCE2A 6 150937463 150938542 12.5 0.129 rs1332498 0.063 70.9 1.0E−04 rs1332498 3.3E−05  10 ERLIN1 6 101899836 101935804 32.3 0.002 rs10883447 2.3E−04 45.8 1.1E−04 rs10883447 1.7E−04  1 LCE2B 8 150925222 150926500 12.9 0.209 rs1332498 0.063 71.0 1.2E−04 rs1332498 3.3E−05 Meta-analysis of gene-based GWAS in southern Chinese and Europeans In the gene-based GWAS of spine BMD in Europeans, C6orf97 had an empirical p value of 0. If there were no simulated test statistics greater than the observed test statistics, the empirical p value would be 0. We replaced the “0” with 1 × 10−6 for the purpose of meta-analysis and applied weighted Z-transformed test to combine the p values of each gene with weighting of sample size of each study.