Table 3.

List of SNPs exceeding the genome-wise significance threshold (P = 5.45E-09) and the suggestive significance threshold (P = 5.00E-07) for the YSL and YFD traits

Trait1	Chr	Position	Ref	Alt	Candidate gene	Distance	P value	Effect
YSL	8	8641258	T	G	FAM46A	intergenic (dist=17641)	1.77E-08	0.36
	8	8641623	C	A	FAM46A	intergenic (dist=17276)	2.80E-08	0.36
	8	8641539	T	A	FAM46A	intergenic (dist=17360)	9.37E-08	0.34
	10	11152096	T	A	—	—	1.10E-07	−0.67
	3	28662360	A	G	LOC105607652	ncRNA_intronic	1.35E-07	0.43
	5	64605486	G	A	SGCD	intronic	1.43E-07	0.51
	22	14975520	G	A	PLCE1	intronic	1.46E-07	0.40
	16	20699162	T	C	RAB3C	intronic	1.54E-07	0.56
	8	8639864	G	C	—	—	1.57E-07	0.34
	21	1902899	G	T	—	—	1.78E-07	−0.66
	8	30591134	C	T	AIM1	Intronic	2.05E-07	0.54
	21	11812855	T	C	FAT3	intronic	2.49E-07	0.53
	6	94762098	G	A	C6H4orf22	intronic	2.62E-07	−0.32
	2	148667359	A	G	PLA2R1	UTR3	2.73E-07	−0.60
	21	15148252	T	A	ANKRD42	intronic	3.03E-07	−0.33
	3	137153518	A	G	KANSL2	intronic	3.17E-07	0.70
	2	123635120	C	T	ZNF804A	intronic	3.26E-07	0.69
	1	74292684	C	A	DPYD	intergenic (dist=17235)	3.33E-07	0.52
	1	108593576	G	C	LOC101114228, LOC101122569	intergenic (dist=4913,dist=4510)	3.54E-07	0.36
	25	34231711	C	A	—	—	3.54E-07	0.54
	2	149652380	C	T	LOC105607993	downstream (dist=344)	4.05E-07	−0.45
	2	148667427	C	G	PLA2R1	UTR3	4.26E-07	−0.56
	13	24682512	C	A	LOC105611292, PRTFDC1	intergenic (dist=26319,dist=8511)	4.35E-07	−0.77
	4	32636538	G	T	LOC101122517	Intronic	4.44E-07	0.58
	21	42401897	T	A	C21H11orf85, BATF2	intergenic (dist=7695,dist=14155)	4.46E-07	0.63
	7	60170543	A	G	—	—	4.52E-07	−0.49
	2	122794998	C	T	—	—	4.76E-07	0.77
YFD	25	1201090	C	T	—	—	3.74E-12	−0.68
	1	35791750	G	A	LOC106990409	ncRNA_intronic	1.75E-11	−0.42
	2	239362082	A	G	ARID1A	intergenic (dist=36217)	2.01E-11	0.41
	22	47736601	A	G	MGMT	intergenic (dist=43353)	3.75E-11	−0.78
	1	261193346	C	G	U2AF1, CRYAA	intergenic (dist=7077,dist=30262)	5.35E-11	−0.76
	16	945395	C	G	SLIT3	Intronic	1.22E-10	0.53
	2	165483199	A	G	ARHGAP15	Intronic	2.54E-09	−0.47
	6	58999238	G	A	N4BP2	Intronic	5.99E-09	0.32
	15	77422591	G	A	TRNAG-UCC	intergenic (dist=24659)	1.04E-08	0.34
	13	81753224	G	A	LOC105611432	intergenic (dist=13119)	1.13E-08	0.58
	19	15779888	G	T	LOC105603404	intergenic (dist=13359)	1.18E-08	−0.63
	13	51218682	A	G	SLC4A11	UTR3	2.22E-08	−0.30
	5	98901530	G	C	—	—	7.58E-08	−0.43
	18	22871804	A	C	LOC105603112	intergenic (dist=25116)	2.19E-07	0.35
	7	84539935	G	A	—	—	2.40E-07	−0.30
	13	65685700	T	G	LOC105606895	ncRNA_intronic	2.66E-07	0.37
	10	34025023	C	T	LOC101115632	intergenic (dist=40244)	3.74E-07	−0.34

¹YSL, yearling staple length; YFD, yearling mean fiber diameter; Distance, The base distance between the significant site and the candidate gene.