Table 1.

Novel Variants from Single-SNV Association Tests

Locus	BMD Phenotype	SNP	Effect Allele	Discovery Meta-Analysis				Replication Meta-Analysis				Combined Meta-analysis
				N	β	P	I2	N	β	P	I2	Freq.	N	β	P	I2
EN1	Lumbar Spine	rs11692564	T	25,225	0.24	4.1×10−9	0.37	15,291	0.20	2.8×10−6	0.46	0.016	40,516	0.22	1.7×10−14	0.40
	Lumbar Spine	rs188303909	T	25,225	0.18	1.7×10−6	0.36	15,228	0.14	3.3×10−4	0.13	0.019	40,453	0.16	1.3×10−9	0.21
	Lumbar Spine	rs6542457	C	25,225	0.08	6.5×10−6	0.00	15,240	0.09	1.5×10−4	0.00	0.058	40,465	0.09	2.2×10−9	0.00
	Femoral Neck	rs55983207	C	29,188	0.10	2.5×10−7	0.19	16,248	0.17	9.8×10−10	0.03	0.042	45,436	0.12	7.2×10−15	0.23
SOX6	Femoral Neck	rs11024028	G	29,188	0.06	2.2×10−8	0.00	15,397	0.03	2.6×10−2	0.30	0.198	44,585	0.05	1.3×10−9	0.04
WNT16	Forearm	rs148771817	T	7,848	0.47	9.3×10−9	0.15	2,539	0.41	5.5×10−4	-	0.012	10,387	0.46	1.1×10−11	0.00

β is the additive effect of the Effect Allele and is measured in standard deviations of bone mineral density