Table 3.

Significant SNP Associations With Trabecular Volumetric BMD at the Femoral Neck

				Discovery sample		Validation sample		Pooled sample
				Adjustment 1b		Adjustment 1b		Adjustment 1b		Adjustment 2c
Gene	SNP	Allele	Frequencya	β	P value	β	P value	β	P value	β	P value	r2 d
APC	rs459552	T→A	0.23	0.006	.018 add	0.004	.049 add	0.004	.005 add	0.004	.006 add	0.004
APC	rs4705573	A→G	0.48	−0.007	.049 rec	−0.007	.012 rec	−0.007	.002 rec	−0.007	.002 rec	0.005
ATF2	rs4972738	G→A	0.37	−0.011	.012 rec	−0.007	.054 rec	−0.009	.001 rec	−0.009	.001 rec	0.005
BMP3	rs2903746	A→T	0.18	0.006	.023 add	0.005	.011 add	0.005	.002 add	0.005	.003 add	0.004
BMP3	rs6814223	G→A	0.13	0.007	.039 add	0.006	.016 add	0.005	.007 add	0.006	.006 add	0.004
BMP7	rs6127983	A→G	0.36	−0.009	.053 rec	−0.007	.040 rec	−0.008	.008 rec	−0.007	.007 rec	0.004
FGF18	rs9313543	G→A	0.19	−0.017	.029 rec	−0.005	.018 add	−0.004	.013 add	−0.004	.019 add	0.003
FLT1	rs1408245	C→G	0.17	−0.026	.008 rec	−0.006	.003 add	−0.017	.002 rec	−0.016	.003 rec	0.004
TGFB3	rs7149264	A→C	0.15	0.006	.034 add	0.004	.050 add	0.005	.008 add	0.005	.011 add	0.003
THRB	rs1505289	A→G	0.43	−0.004	.048 add	−0.004	.034 add	−0.004	.003 add	−0.004	.003 add	0.004
RUNX1	rs2834676	G→A	0.42	0.005	.030 add	0.010	.003 rec	0.004	.003 add	0.007	.002 rec	0.005
RUNX1	rs2834694	C→A	0.49	0.006	.007 add	0.011	1.4 × 10−4 rec	0.010	5.3 × 10−6 rec	0.010	4.2 × 10−6 rec	0.010

Note: Additive (add) and recessive (rec) models were tested for each SNP, and the regression parameter and p value from the most significant genetic model (additive or recessive) are shown.

add = p value from the additive model; rec = p value from recessive model.

^aMinor allele frequency in the pooled sample.

^bAdjustment 1: Age, clinic site, population substructure.

^cAdjustment 2: Age, clinic site, population substructure, height, body weight.

^dAmount of variation explained after adjusting for age, site, population substructure, height, body weight.