Table 3 Loci associated with bone traits in crossbred layer population.

Chromosome	SNP	Physical position^a	Minor/major Allele	Minor Allelic Frequency	Candidate gene	SNP location	Proportion phenotypic variance	Beta^b	SE^c	P Value	Trait
1	rs312784357	165885243	A/G	0.480	RANKL	intergenic	0.050	-0.298	0.057	3.09E-07	BMC
1	rs312550725	169381724	T/C	0.405	SERPINE3	missense	0.013	0.226	0.047	4.71E-08	Breaking strength
1	rs317281616	169400244	G/A	0.307	INTS6	intron	0.030/0.056	0.275/0.345	0.049/0.055	1.29E-08/5.86E-10	Breaking work/BMC
1	rs13975174	171298203	A/G	0.370	POSTN	intron	0.077	−0.293	0.050	2.88E-12	Femoral weight
4	rs14491507	76073771	A/G	0.052	TAPT1	intergenic	0.024	0.479	0.090	1.11E-07	BMC
4	rs15620367	76186390	A/G	0.130	FGFBP1	intron	0.023	0.333	0.066	5.51E-07	Femoral weight
14	rs313699988	11876668	T/C	0.126	GSG1L	intergenic	0.023	0.315	0.062	4.18E-07	BMD
24	rs315096388	1684374	T/C	0.177	ADAMTS15	intergenic	0.014	0.215	0.051	2.43E-07	Breaking strength
27	rs316237751	3200813	G/C	0.087	SOST	intergenic	0.031	0.430	0.071	1.59E-09	BMC
27	rs316723909	3464323	G/A	0.087	IGF2BP1	intergenic	0.041	0.500	0.072	5.01E-12	Femoral weight

^aPhysical position is bp location on chromosome for NCBI Gallus_gallus-4.0. ^bEstimates presented for allelic substitution effect per copy of the effect allele (EA) under an additive model, expressed in SD unit/allele.
^cSE is the standard error of the beta.

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