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

Table 1 Mapping of bovine candidate enhancers

db^a	Query^b			Met^f	m%^g	Hits^h			eSNP^l
db^a	ISeq^c	u (bp)^d	σ (bp)^e	Met^f	m%^g	OSeqⁱ	µ (bp)^j	σ (bp)^k	eSNP^l
VISTA	4481	1959	1395	COM	4285 (96%)	9945	896	710	82,865
				LO	3808 (85%)	964	1399	883
				BN	3627 (81%)	9945	896	710
FANTOM5	109,882	277	158	COM	95,123 (87%)	30,371	231	115	50,447
				LO	94,302 (86%)	6061	245	503
				BN	10,054 (9%)	30,389	231	115
dbSUPER	1745	45,750	56,541	COM	1605 (92%)	50,938	739	763	282,285
				LO	1549 (88%)	32	1916	2447
				BN	1113 (64%)	50,938	739	763
H3K4me3	13,797	2393	879	NA	13,797 (100%)	13,660	2394	879	302,659
H3K27ac	45,784	2304	1910	NA	45,784 (100%)	42,963	2305	1910	965,716

^aDatabase from which input query sequences were obtained
^bQuery sequence downloaded from respective host sites (may include overlapping regions)
^cNumber of input enhancer query sequences
^dMean length of input enhancer query sequences (measured in bp)
^eStandard deviation length of input enhancer query sequences (measured in bp)
^fMethod that returned values in column m%; COM: a set of non-overlapping regions from the combined results of liftOver and BLASTn; LO: liftOver; BN: BLASTn
^gNumber of mapped query sequences (ratio of mapped query sequences); NA not applicable
^hHit is a non-overlapping genomic interval in the bovine genome that matches with at least one query sequence from the respective input database
ⁱNumber of non-overlapping candidate bovine enhancer genomic intervals; all hits, i.e. output from the respective software were merged into non-overlapping genomic intervals; some OSeq values were larger than corresponding ISeq values because one query sequence was found at multiple locations in the bovine genome
^jMean length of bovine putative enhancer sequences (measured in bp)
^kStandard deviation length of bovine putative enhancer sequences (measured in bp)
^lNumber of imputed whole-genome sequence variants in OSeq genomic intervals

ISSN: 1297-9686