Table 2.

QTL regions for each of the trait. Top SNP for each QTL are shown including position, -log₁₀(p)-values, minor allele frequency (MAF), gene information, annotation of the top SNP, allele substitution effect (b.value) and standard error for b.value (SE)

CHR	Start (bp)	End (bp)	Length of the QTL region (bp)	Significant SNPs in region	No of genes with significant SNPs within the QTL region	Top SNP	Position of the top SNP (bp)	- log10(p)	MAF	Gene	Annotation of the top SNP	b.value	SE
Fat yield
5	92,372,732	94,425,668	2,052,936	330	3	rs209818856	93,945,694	27.49	0.38	MGST1	intron variant	−2.807	0.253
14	1,448,510	2271832	823,322	509	49	rs136783505	1,807,140	42.01	0.07	DGAT1/HSF1	downstream variant/intron variant	−6.709	0.484
23	28,567,796	28,591,530	23,734	5	1	rs381390819	28,567,796	9.36	0.45	TRIM26	intron variant	1.148	0.184
25	8,222,347	11,507,986	3,285,639	883	16	rs379546164	9,870,005	14.40	0.24	CLEC16A	intron variant	−1.769	0.224
25	36,226,978	36,227,132	154	2		rs109480808	36,226,978	8.72	0.16		intergenic variant	1.635	0.272
26	22,144,777	24,793,744	2,648,967	595	32	rs438420348	24,379,571	14.28	0.16	NEURL1	intron variant	−2.273	0.290
26	44,802,991	44,802,991	0	1		rs135624939	44,802,991	9.72	0.28		intergenic variant	−1.474	0.231
Milk yield
5	112,343,204	11,2450,860	107,656	2	1	rs383553819	112,343,204	8.70	0.36	MKL1	intron variant	1.437	0.239
14	1,448,510	2,271,832	823,322	455	48	rs133033480	1,743,939	33.01	0.09	CPSF1/ADCK5	downstream variant/splice region variant, intron variant	6.266	0.513
16	1,322,611	1,322,611	0	1	1	rs108979795	1,322,611	8.58	0.28	LAX1	upstream variant	−1.451	0.243
19	61,447,138	61,449,096	1958	5		rs210324693	61,449,096	8.93	0.32		intergenic variant	1.490	0.244
20	30,531,217	32,952,019	2,420,802	74	5	rs385640152	31,909,478	15.56	0.11	GHR	missense variant	−3.877	0.472
20	37,766,226	39,183,141	1,416,915	34	3	NA	38,828,254	9.54	0.16		intergenic variant	−2.250	0.356
25	2,669,704	2,669,704	0	1		rs209691835	2,669,704	9.21	0.13		intergenic variant	−2.855	0.460
25	3,494,706	3,516,671	21,965	13	4	rs110749311	3,498,960	9.32	0.41	PAM16/GLIS2	downstream variant	1.225	0.196
Protein yield
5	112,450,860	112,450,860	0	1		rs109041054	112,450,860	8.88	0.48		intergenic variant	−1.473	0.242
14	1,802,667	1,802,667	0	1	2	NA	1,802,667	8.52	0.06	DGAT1/HSF1	intron variant/downstream variant	3.354	0.564
25	1,094,996	1,257,612	162,616	12	3	rs136085792	1,103,856	10.83	0.22	UNKL	intron variant	1.694	0.250
25	3,306,363	3,516,671	210,308	40	8	rs110749311	3,498,960	11.70	0.41	PAM16/GLIS2	downstream variant	1.427	0.202