Table 3.

Genome-wide significant SNPs for CE and suggestive genome-wide significant SNPs for BT and NG

SNP	Analysis	Location (ECA:bp)	MAF	β	SE	Var (%)	Nearest gene	Distance to nearest gene (bp)	Raw p-value
AX-104828170	CE	28:20,006,740	0.018	−3.380	0.552	3.85	NDUFA12	114,732	9.01E-10
AX-103147507	CE	28:22,153,465	0.005	−5.762	1.011	3.27	ENSECAG00000025907	46,196	1.20E-08
AX-104611735	CE	6:47,132,529	0.015	−3.407	0.599	3.16	PDE3A	0	1.28E-08
AX-104865129	CE	16:18,366,321	0.008	−4.488	0.798	3.17	ENSECAG00000003087/PROK2	138,149/138,791	1.87E-08
AX-104494389	CE	6:20,020,914	0.006	−4.557	0.825	3.32	INPP5D	0	3.36E-08
AX-103248294	CE	6:49,512,490	0.016	−3.166	0.582	3.11	SOX5	0	5.28E-08
AX-103090138	CE	6:42,063,985	0.018	−3.007	0.559	2.46	PLBD1	3191	7.48E-08
AX-104711589	CE	6:41,462,481	0.012	−3.497	0.657	2.59	GRIN2B	0	9.99E-08
AX-104307051	CE	6:41,329,519	0.012	−3.474	0.657	2.67	GRIN2B	0	1.21E-07
AX-104144838	NG	23:23,333,501	0.278	−0.214	0.046	1.51	ENSECAG00000023609	187,643	3.18E-06
AX-104568609	NG	1:159,285,045	0.004	−1.343	0.293	1.14	ENSECAG00000003696/ENSECAG00000022264	19,813/25,804	4.52E-06
AX-102982528	NG	23:23,324,996	0.412	−0.186	0.041	1.27	ENSECAG00000023609	179,138	6.74E-06
AX-103734745	NG	29:24,530,437	0.453	−0.176	0.040	1.29	ENSECAG00000004576	944,126	8.67E-06
AX-104373992	BT	1:162,993,722	0.016	3.289	0.655	1.79	ENSECAG00000023062/ENSECAG00000008721	32,728/51,254	5.10E-07
AX-103261370	BT	23:22,522,071	0.409	−0.910	0.183	0.87	DOCK8	0	6.49E-07
AX-104219924	BT	17:19,525,955	0.279	0.946	0.197	2.24	WDFY2	0	1.57E-06
AX-104634248	BT	23:21,857,316	0.108	1.346	0.284	1.21	PIP5K1B/FAM122A	14,893/18,794	2.20E-06
AX-103287280	BT	23:21,064,571	0.117	1.270	0.268	1.49	PTAR1	43,300	2.22E-06
AX-104645782	BT	17:19,318,167	0.258	0.951	0.201	2.21	ATP7B	0	2.32E-06
AX-103762427	BT	23:22,461,979	0.154	−1.156	0.245	1.37	DOCK8	0	2.45E-06
AX-103530176	BT	23:22,464,604	0.156	−1.139	0.246	1.25	DOCK8	0	3.49E-06
AX-103445942	BT	1:151,919,692	0.012	3.600	0.777	1.39	ENSECAG00000012236/ENSECAG00000013533	74,605/78,356	3.63E-06
AX-104538418	BT	17:21,083,126	0.279	0.905	0.196	2.29	KCNRG	0	3.99E-06
AX-104268231	BT	23:21,689,609	0.385	−0.823	0.179	0.79	PIP5K1B	0	4.25E-06
AX-102964033	BT	23:22,423,197	0.121	−1.259	0.275	0.95	DOCK8	5699	4.59E-06
AX-104117851	BT	7:65,266,179	0.010	3.724	0.821	1.76	ENSECAG00000007398	162,661	5.78E-06
AX-104642194	BT	31:14,300,483	0.006	4.612	1.021	1.37	MTRF1L/FBXO5	108/14,491	6.31E-06
AX-103166989	BT	23:22,496,787	0.116	−1.270	0.283	0.99	DOCK8	0	7.07E-06
AX-103803214	BT	2:21,466,714	0.049	1.725	0.386	1.82	AGO1	2494	7.72E-06
AX-104450418	BT	2:21,311,680	0.087	1.351	0.304	1.93	TEKT2/ADPRHL2	10,587/14,440	9.00E-06
AX-103305676	BT	25:26,866,219	0.019	2.590	0.584	1.67	OR1L3	492	9.11E-06
AX-104591507	BT	17:20,813,164	0.249	0.898	0.203	1.84	KCNRG	227,34	9.36E-06

CE career earnings, BT Best km time, NG number of gallop, MAF Minor allele frequency, β Estimated allele substitution effect, Var (%) Percentage of phenotypic variance explained

Red line = Bonferroni threshold (P < 1.39 × 10⁻⁷)