Table 1.

The number of significant SNPs (- log₁₀(p) ≥8.50) for each trait and how SNPs are divided into different consequences. SNPs were annotated with the variant effect predictor –tool [28]. One SNP can have more than one annotation

Trait	Number of significant SNPs	Intron variant	Intergenic variant	Downstream gene variant	Upstream gene variant	Synonymous variant	Missense variant	3′ UTR variant	Splice region variant, intron variant	5′ UTR variant	Splice region variant, synonymous variant
Fat yield	3594	1641	1307	600	551	94	40	39	9	6	2
Milk yield	755	322	195	301	240	42	20	16	5	1	2
Prot. yield	85	50	14	32	12	3	3	1	1