A validation of the first genome-wide association study of calcaneus ultrasound parameters in the European Male Ageing Study

Roshandel, Delnaz; Thomson, Wendy; Pye, Stephen R; Boonen, Steven; Borghs, Herman; Vanderschueren, Dirk; Huhtaniemi, Ilpo T; Adams, Judith E; Ward, Kate A; Bartfai, Gyorgy; Casanueva, Felipe; Finn, Joseph D; Forti, Gianni; Giwercman, Aleksander; Han, Thang S; Kula, Krzysztof; Lean, Michael E; Pendleton, Neil; Punab, Margus; Silman, Alan J; Wu, Frederick C; Holliday, Kate L; O'Neill, Terence W

doi:10.1186/1471-2350-12-19

Table 2 Characteristics of the SNPs and their association with BUA and SOS

From: A validation of the first genome-wide association study of calcaneus ultrasound parameters in the European Male Ageing Study

						Adjusted for centre				Adjusted for centre, age, BMI, height, smoking and PASE score
						BUA		SOS		BUA		SOS
Chr	Position	SNP	Alleles	MAF (%)	Nearest Gene within 500 kb	β (SD)	p	β (SD)	p	β (SD)	p	β (SD)	p
1	55553409	rs1807871	T > C	13.1	USP24	0.00	0.949	0.00	0.988	-0.02	0.645	0.00	0.949
1	92085352	rs2799516	G > A	9.0	TGFBR3	0.04	0.455	0.05	0.347	0.02	0.694	0.04	0.386
1	92099224	rs2046737	C > T	8.5	TGFBR3	0.06	0.231	0.06	0.240	0.05	0.339	0.06	0.267
1	111784127	rs3754032	T > A	26.0	WDR77	0.02	0.505	0.07	0.032	0.01	0.665	0.06	0.085
2	70027133	rs10496176	T > C	15.4	MXD1	0.03	0.440	0.01	0.874	0.02	0.619	0.00	0.950
2	82913481	rs10496276	T > G	19.2		0.02	0.638	0.01	0.696	0.00	0.944	0.00	0.940
2	118250857	rs1433527	C > A	45.3	DDX18	-0.04	0.110	-0.04	0.211	-0.05	0.081	-0.03	0.262
2	135824309	rs10496734	G > A	14.9	ZRANB3	-0.04	0.363	-0.03	0.447	-0.06	0.172	-0.06	0.139
2	158955976	rs2251471	T > C	6.7	CCDC148	0.09	0.123	0.12	0.027	0.10	0.060	0.14	0.012
3	30344099	rs1587126	A > C	33.7	TGFBR2	0.01	0.769	-0.01	0.665	-0.01	0.856	-0.02	0.496
3	99203733	rs1492053	G > A	37.0	GABRR3	0.00	0.963	0.00	0.909	0.01	0.704	0.01	0.674
3	163243925	rs10513577	T > C	31.0		0.00	0.991	0.01	0.773	0.02	0.559	0.03	0.320
3	163273126	rs1033059	A > G	31.0		0.00	0.943	0.01	0.815	0.02	0.588	0.03	0.339
3	163310228	rs951937	T > A	25.6		-0.02	0.568	0.00	0.975	-0.01	0.873	0.01	0.665
4	9933258	rs9291683	G > A	46.8	ZNF518B	0.04	0.171	0.04	0.168	0.03	0.334	0.03	0.245
4	57967285	rs10517393	G > T	22.8	IGFBP7	0.01	0.795	-0.03	0.341	0.02	0.481	-0.02	0.639
4	132163115	rs2055391	C > T	8.4		-0.01	0.920	0.00	0.996	0.01	0.789	0.01	0.800
4	182246126	rs7659755	A > G	18.3		-0.02	0.534	-0.04	0.225	-0.01	0.889	-0.03	0.366
5	54231548	rs2099082	T > C	23.6	ESM1	0.00	0.903	-0.01	0.767	0.01	0.853	0.00	0.957
5	157166116	rs10515754	T > C	6.0	CLINT1	0.06	0.293	0.05	0.422	0.10	0.086	0.10	0.082
6	91568115	rs9294466	A > T	15.0	MAP3K7	0.04	0.301	0.05	0.211	0.05	0.172	0.06	0.129
6	96483564	rs6925466	C > T	38.9	FUT9	0.00	0.870	0.00	0.888	-0.02	0.503	-0.02	0.493
7	14495103	rs7786503	A > C	8.0	DGKB	0.02	0.643	0.02	0.759	0.02	0.672	0.02	0.722
7	14497256	rs10499444	C > G	7.7	DGKB	0.01	0.869	-0.01	0.898	0.01	0.884	0.00	0.942
7	30896348	rs6462230	G > C	10.7	FLJ22374	0.04	0.396	0.06	0.221	0.02	0.732	0.03	0.485
7	147333625	rs2214681	G > A	42.5	CNTNAP2	0.00	0.950	-0.01	0.723	-0.01	0.798	-0.02	0.476
10	59991493	rs1649053	T > C	38.8	BICC1	-0.02	0.583	-0.01	0.829	-0.04	0.151	-0.03	0.324
10	127169837	rs10510144	G > A	28.9	MMP21	0.05	0.127	0.06	0.048	0.05	0.083	0.08	0.016
13	20860773	rs1409071	G > A	41.9	ZDHHC20	0.05	0.106	0.06	0.047	0.02	0.559	0.03	0.288
13	41736674	rs238358	G > A	9.5	AKAP11	0.03	0.536	0.03	0.516	-0.01	0.916	-0.01	0.896
13	92478066	rs10492621	G > A	24.2	GPC5	-0.06	0.068	-0.07	0.042	-0.07	0.035	-0.07	0.045
14	86696500	rs10513893	C > T	7.2		0.01	0.830	-0.01	0.821	0.04	0.449	0.03	0.551
16	26362052	rs8049649	A > T	17.6	HS3ST4	0.06	0.080	0.05	0.197	0.06	0.103	0.05	0.191
20	23097739	rs10485640	A > G	9.7	CD93	-0.05	0.274	-0.05	0.334	-0.05	0.273	-0.06	0.187

Chr: Chromosome, MAF: Minor allele frequency, BUA: Broadband ultrasound attenuation, SOS: Speed of sound, PASE: Physical activity scale for the elderly; β(SD), effect estimates are shown as standardized values (standard deviations) for each copy of the minor allele.

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ISSN: 1471-2350

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