Table 2.

Summary of SNPs linked (LOD>2.50) in the MALD analysis of vitamin D concentrations, parathyroid hormone concentrations, and bone mineral density with fine-mapping from GWAS data in the AA-DHS sample.

				Allele frequency			MALD		GWAS
Locus	SNP	Gene	Alleles1	Observed2	CEU3	YRI4	Model	LOD Score	n5	Beta±SE	P-value6	R27
1,25-dihydroxyvitamin D
13q21.2	rs1622710		A/G	0.73	0.05	0.83	Recessive	3.20
	rs183787871	PCDH20/-	C/T	0.01					34937	2.07±0.53	9.12E-05	0.06
12q13.2	rs11171526		T/A	0.34	0.97	0.23	Additive	3.10
	rs10783612	CALCOCO1/HOXC13	C/T	0.42					39571	−0.34±0.08	2.52E-05	0.05
4p15.32	rs2872795		C/T	0.23	0.83	0.14	Additive	2.82
	rs144095555	FAM184B	C/T	0.01					25896	−0.39±0.11	2.18E-04	0.001
Vitamin D Binding Protein
4q13.3	rs7689609		A/G	0.14	0.93	0.00	Additive	11.05
	rs7041	GC	C/A	0.15					4472	0.52±0.02	1.38E-82	0.52
2q35	rs16859382		A/G	0.38	1.00	0.19	Recessive	2.64
	rs719325	SLC4A3/-	T/C	0.33					145403	−0.09±0.02	2.91E-05	0.03
1q32.2	rs979698		A/G	0.76	0.18	0.9	Additive	2.54
	rs1284852	FLVCR1/VASH2	A/G	0.61					4930	−0.079±0.021	1.33E-04	0.03
	rs4951471	FLVCR1/VASH2	A/G	0.61						−0.079±0.021	1.33E-04	0.03
Bioavailable Vitamin D
17q12	rs739753		A/T	0.25	0.81	0.15	Dominant	2.58
	rs4375714	FAM134C	T/C	0.46					26458	−0.06±0.01	1.03E-04	0.03
Intact parathyroid hormone
9q31.3	rs7854368		A/G	0.29	0.74	0.17	Additive	3.14
	rs10125548	KLF4/ACTL7B	A/G	0.70					7395	−0.13±0.03	7.81E-05	0.03
1q42.2	rs701185		A/C	0.22	0.71	0.06	Recessive	2.69
	rs623448		G/A	0.07					4006	−0.22±0.06	1.46E-04	0.02
Lumbar Volumetric Bone Mineral Density
15q11.2	rs2719890		A/G	0.73	0.03	0.88	Dominant	2.52
	rs8040786	NDN/PWRN2	A/G	0.06					927	0.61±0.18	5.90E-4	0.01

¹Reference/other allele,

²AA-DHS (n_max=552),

³CEPH (Utah Residents with Northern and Western European Ancestry) (n=60),

⁴Yoruba in Ibadan, Nigeria (n=60),

⁵number of variants (directly genotyped and imputed) in the LOD-1 confidence interval,

⁶Additive model,

⁷Variation in phenotype explained by the genetic variant