Table 1.

Index SNPs of Loci Not Previously Associated with BMD

CHR	BP	rs Number	Locus	A1	A2	EAF	Effect	p	N	Annotation	Closest Gene	Notes	LS-beta	LS-P	FN-beta	FN-P
1	8422676	rs2252865	1p36.23	T	C	0.32	−0.033	4.72 × 10−8	66,075	intronic	RERE	novel biology	−0.019	0.043	−0.025	0.002
1	110475971	rs7548588	1p13.3	T	C	0.61	−0.037	9.29 × 10−8	66,240	intergenic	CSF1	osteoclast differentiation39	−0.030	0.001	−0.022	0.005
1	220038825	rs185048405	1q41	T	C	0.54	0.042	3.07 × 10−8	66,540	intronic	SLC30A10	manganese transport40	−0.035	0.076	−0.003	0.878
2	27741072	rs780096	2p23.3	C	G	0.44	−0.031	4.58 × 10−8	66,578	intronic	GCKR	calcium regulation,41 hepatic traits42	−0.014	0.129	−0.017	0.029
2	40630678	rs10490046	2p22.1	A	C	0.76	0.043	1.43 × 10−10	65,961	intronic	SLC8A1	bone mineralization43	0.015	0.162	0.021	0.025
2	68962137	rs10048745	2p13.3	A	G	0.25	−0.039	6.44 × 10−8	66,565	5′ UTR	ARHGAP25	novel biology	−0.050	1.03 × 10−6	−0.036	5.21 × 10−5
2	85484818	rs11904127	2p11.2	A	G	0.55	−0.032	2.65 × 10−8	66,561	intronic	TCF7L1	factors in Wnt signaling44	−0.021	0.023	−0.015	0.054
2	198874006	rs1595824	2q33.1	T	C	0.47	0.034	2.65 × 10−8	60,171	intronic	PLCL1	negative regulation of bone formation45	0.022	0.201	0.052	2.20 × 10−4
2	202799604	rs2350085	2q33.2	T	C	0.87	−0.064	3.80 × 10−14	66,412	intergenic	FZD7	factors in Wnt signaling46	−0.042	0.002	−0.044	1.96 × 10−4
2	234303405	rs838721	2q37.1	A	G	0.44	−0.031	4.48 × 10−8	65,516	intronic	DGKD	calcium regulation41	−0.016	0.070	−0.014	0.068
5	112221869	rs818427	5q22.2	T	C	0.31	0.034	2.37 × 10−8	66,592	intronic	APC	bone metabolism47	0.004	0.645	0.008	0.327
5	122847622	rs11745493	5q23.2	A	G	0.75	0.044	7.75 × 10−12	66,597	promoter	CSNK1G3	novel biology	0.010	0.326	0.025	0.005
7	27989403	rs757138	7p15.1	T	G	0.69	−0.035	3.33 × 10−8	66,043	intronic	JAZF1	novel biology	−0.016	0.126	−0.025	0.004
7	30957702	rs28362721	7p14.3	T	C	0.18	−0.059	6.71 × 10−14	66,274	intronic	AQP1	bone metabolism48	−0.037	0.002	−0.049	1.39 × 10−6
7	50901491	rs1548607	7p12.1	A	G	0.69	0.036	4.18 × 10−8	66,564	intergenic	GRB10	novel biology	0.034	5.59 × 10−4	0.005	0.517
7	99130834	rs34670419	7q22.1	T	G	0.04	−0.088	1.09 × 10−8	66,336	3′ UTR	ZKSCAN5	DHEAS and aging mechanisms49	−0.127	9.28 × 10−8	−0.080	8.19 × 10−5
10	112245400	rs73349318	10q25.2	A	T	0.87	−0.047	2.68 × 10−8	66,341	intronic	DUSP5	osteoclast differentiation50	−0.042	0.001	−0.051	8.76 × 10−6
10	124015986	rs10788264	10q26.13	A	G	0.48	−0.034	2.61 × 10−8	66,565	intergenic	TACC2	novel biology	−0.030	9.64 × 10−4	−0.029	1.29 × 10−4
11	242859	rs55781332	11p15.5	A	G	0.78	−0.055	8.07 × 10−16	66,198	intronic	PSMD13	novel biology	−0.046	1.76 × 10−5	−0.026	0.005
11	35083633	rs2553773	11p13	C	G	0.41	−0.037	1.49 × 10−10	66,619	intergenic	CD44	osteoclast activity51	−0.015	0.101	−0.015	0.054
11	35981346	rs113964474a	11p.13∗	A	G	0.03	0.485	1.41 × 10−8	6,748	intronic	LDLRAD3	novel biology	–	–	–	–
11	69299537	rs4980659	11q13.3	C	G	0.52	0.033	1.16 × 10−8	66,537	intergenic	CCND1	target of Wnt signaling52	0.039	1.58 × 10−5	0.023	0.003
11	121913230	rs725670	11q24.1	A	G	0.38	−0.032	3.61 × 10−8	66,565	intergenic	BLID	novel biology	−0.020	0.028	−0.011	0.172
12	90334829	rs10777212	12q21.33	T	G	0.35	0.045	5.05 × 10−14	66,619	intergenic	ATP2B1	calcium absorption53	0.028	0.003	0.021	0.010
12	116555786	rs73200209b	12q24.21	A	T	0.80	0.045	2.51 × 10−8	51,240	intronic	MED13L	novel biology	0.030	0.167	0.036	0.044
13	37487021	rs556429	13q13.3	A	C	0.23	0.039	1.46 × 10−8	66,504	intronic	SMAD9	osteoblast differentiation54	0.023	0.027	0.013	0.135
15	38340874	rs12442242	15q14	A	G	0.85	−0.051	4.94 × 10−10	66,403	intergenic	TMCO5A	novel biology	−0.046	3.03 × 10−4	−0.047	2.26 × 10−5
15	51537806	rs2414098	15q21.2	T	C	0.39	−0.033	1.99 × 10−8	66,562	intronic	CYP19A1	estrogen byosynthesis55	−0.034	0.007	−0.038	0.001
15	67420680	rs1545161	15q22.33	A	G	0.56	0.041	1.06 × 10−12	66,004	intronic	SMAD3	osteoblast differentiation56	0.034	1.27 × 10−4	0.035	5.78 × 10−6
17	17804725	rs8070128	17p11.2	T	C	0.58	−0.039	1.98 × 10−11	66,625	intronic	TOM1L2	novel biology	−0.033	4.80 × 10−4	−0.015	0.052
17	63771079	rs9972944	17q24.1	A	G	0.41	0.036	6.87 × 10−10	66,595	intronic	CEP112	novel biology	0.028	0.003	0.004	0.576
19	31654615	rs6510186c	19q12	T	C	0.26	0.068	3.11 × 10−8	18,782	intergenic	TSHZ3	novel biology	0.004	0.713	0.006	0.492
20	39103882	rs6029130	20q12	T	C	0.30	0.035	3.50 × 10−8	66,497	intergenic	MAFB	osteoclast differentiation57	0.027	0.007	0.015	0.083
21	28773868	rs1452102	21q21.3	T	G	0.59	−0.035	1.74 × 10−8	66,489	intergenic	ADAMTS5	endochondral ossification58	−0.029	0.001	−0.015	0.056
21	36970350	rs9976876	21q22.12	T	G	0.45	−0.038	8.01 × 10−11	66,514	intronic	RUNX1	osteoclast differentiation59	−0.019	0.031	−0.016	0.041
21	40350744	rs11910328	21q22.2	A	G	0.84	−0.043	2.99 × 10−8	66,298	intergenic	ETS2	osteoblast maturation60	−0.028	0.020	−0.028	0.007

Variants associated with TB-BMD in the all-ages combined meta-analysis that map outside ±500 kb of known index SNPs of genetic associations with different bone traits. Genomic coordinates are on build 37 of the human genome. Notes refer to annotation based on the closest gene. Associations with lumbar spine (LS) and femoral neck (FN)-BMD.⁹ Beta coefficients and allele frequencies (EAF) are reported for the A1 allele.

^aMonomorphic in European cohorts

^bReported statistics from the in the meta-analysis of European populations

^cReported statistics from the meta-analysis in the 30–45 age strata