Putative enhancer sites in the bovine genome are enriched with variants affecting complex traits

Table 5 Enrichment of significant enhancer SNPs \(\left( {P \le 10^{ - 8} } \right)\) for milk production traits in the permutation tests

Phenotype	Database	All SNPs/a subset of SNPs	Fold change^a	Rank^b
FY	VISTA	All	0.16235	0.0001
MY			0.336793	0.0001
PY			0	0.0001
FY	FANTOM5		0.200888	0.0001
MY			0.414773	0.0018
PY			0.096781	0.0001
FY	dbSUPER		0.226716	0.0001
MY			0.354855	0.0001
PY			0.329258	0.0001
FY	Villar (H3K4me3)		2.892337	<0.0001
MY			2.100798	<0.0001
PY			3.081699	<0.0001
FY	Villar (H3K27ac)		1.459357	<0.0001
MY			1.29579	<0.0001
PY			1.458739	<0.0001
FY	Villar:H3K4me3	H3K4me3-specific only	3.358042	<0.0001
MY			2.440737	<0.0001
PY			4.414017	<0.0001
FY	Villar:H3K27ac	H3K27ac-sepcific only	0.967677	0.3063
MY			1.023431	0.647
PY			0.953471	0.2794
FY	Villar:H3K4me3 and H3K27ac	Overlaps: H3K4me3 and H3K27ac	2.795722	<0.0001
MY			2.025759	<0.0001
PY			2.801491	<0.0001

^aFold change is the ratio between the actual number of significant SNPs in an enhancer set and the mean number of all significant SNPs in the 10,000 random samples
^bRanking position of the actual number of significant SNPs in an enhancer set within the distribution of all the numbers of significant SNPs for the 10,000 random samples; if the actual number of significant SNPs was the largest among all the numbers of the 10,000 random significant SNPs, the rank was set to <0.0001; otherwise it was denoted as the ranking position of the actual number of significant SNPs among the number of random significant SNPs

ISSN: 1297-9686