Table 1. Five loci are associated with bone mineral density in children, with two loci (IZUMO3 and SPBT) showing sex-specific associations.

Summary statistics for top signals achieving genome-wide significance in the combined analysis (discovery plus replication) for BMD at four skeletal sites (1/3 distal radius, total hip, femoral neck and spine). Effect sizes (betas) refer to the minor allele. Genomic positions are reported in the GRCh37/hg19 build. The significance threshold for the test of sex heterogeneity is set at 4×10⁻³.

Associated Loci						Females					Males					All					Het Test
SNP (Locus, Pos)	Nearest Gene	Major Allele	Minor Allele	Trait	Stage	MAF	Beta	SE	P-value	N	MAF	Beta	SE	P-value	N	MAF	Beta	SE	P-value	N	P-value
rs6963115	CPED1	C	A	Radius	Discovery	0.398	−0.402	0.060	7.49×10−11	474	0.393	−0.133	0.069	5.43×10−2	434	0.395	−0.274	0.047	5.95×10−9	908	3.42×10−3
7q31.31					Replication	0.378	−0.171	0.081	3.62×10−2	242	0.427	−0.294	0.091	1.45×10−3	239	0.402	−0.230	0.061	1.90×10−4	481	3.11×10−1
chr7:120825318					Combined	0.391	−0.331	0.049	2.40×10−11	716	0.405	−0.189	0.055	6.75×10−4	673	0.398	−0.260	0.037	3.89×10−12	1389	5.48×10−2
rs184374109	IZUMO3	C	A	Spine	Discovery	0.042	0.114	0.160	4.76×10−1	485	0.057	0.727	0.147	1.02×10−6	442	0.050	0.447	0.110	5.53×10−5	927	4.81×10−3
9p21.3					Replication	0.028	−0.279	0.325	3.91×10−1	240	0.037	0.760	0.254	3.11×10−3	239	0.033	0.322	0.203	1.13×10−1	479	1.17×10−2
chr9:25069552					Combined	0.038	0.020	0.145	8.92×10−1	725	0.050	0.737	0.128	1.18×10−8	681	0.044	0.411	0.097	2.57×10−5	1406	2.13×10−4
chr16:7788155:D	RBFOX1	CG	C	Spine	Discovery	0.260	−0.153	0.067	2.23×10−2	485	0.238	−0.253	0.101	1.32×10−2	442	0.254	−0.191	0.049	1.19×10−4	927	4.11×10−1
16p13.3					Replication	0.249	−0.315	0.100	1.85×10−3	240	0.248	−0.247	0.071	5.45×10−4	239	0.243	−0.283	0.071	8.15×10−5	479	5.81×10−1
chr16:7788155					Combined	0.256	−0.208	0.056	2.19×10−4	725	0.244	−0.245	0.058	2.84×10−5	681	0.250	−0.224	0.041	4.06×10−8	1406	6.41×10−1
rs1957429	SPTB	C	T	Radius	Discovery	0.131	0.402	0.095	2.94×10−5	474	0.097	−0.004	0.163	9.80×10−1	434	0.118	0.208	0.075	5.33×10−3	908	3.10×10−2
14q23.3					Replication	0.117	0.510	0.122	4.30×10−5	242	0.105	−0.004	0.114	9.71×10−1	239	0.107	0.296	0.100	3.31×10−3	481	2.11×10−3
chr14:65354033					Combined	0.126	0.444	0.075	5.97×10−9	716	0.102	−0.006	0.094	9.51×10−1	673	0.114	0.241	0.060	5.90×10−5	1389	1.77×10−4
rs34652660	TBPL2	A	C	Femoral Neck	Discovery	0.486	−0.243	0.056	1.92×10−5	485	0.477	−0.085	0.079	2.79×10−1	443	0.479	−0.217	0.042	3.05×10−7	928	1.04×10−1
14q22.3					Replication	0.463	−0.237	0.091	1.01×10−2	242	0.471	−0.178	0.060	3.19×10−3	240	0.470	−0.158	0.060	9.15×10−3	482	5.87×10−1
chr14:55919480					Combined	0.478	−0.240	0.048	7.22×10−7	727	0.473	−0.147	0.048	2.20×10−3	683	0.476	−0.198	0.035	1.45×10−8	1410	1.70×10−1