Table 2.

The summary of the functional annotation sets in this study

Omics	Partitions (Number of animals)	Targeted variant sets (no. of variants)
Genomic	Conserved 100 species (NA)	Bovine genome sites lifted over from human sites with PhastCon score  > 0.9 calculated using genomes of 100 vertebrate species (192825)
	Annotation (NA)	SnpEff was used to annotate the variants which was annotated as UTR (43,207), intergenic (6,132,394), geneend (863,401), intron (3,096,627), regulatory.related (11,534) and coding.related (66,762)
	Selection signature (44)	Regions at the top 1% with the highest average |iHS| score and SNP numbers greater than 10 were regarded as candidate regions under positive selection (109,325)
	P-variants (NA)	Variants have been identified in cattle: those relating to body size and beef production
	LD (1577)	First quartile (2,553,483), second quartile (2,553,481), third quartile (2,553,486), and fourth quartile (2,553,475)
	Freq (1577)	First quartile (2,557,044), second quartile (2,555,826), third quartile (2,550,339), and fourth quartile (2,550,716)
	Variant density (1577)	First quartile (2,564,482), second quartile (2,564,733), third quartile (2,538,073), and fourth quartile (2,546,637)
Metabolomics	mQTLs (117)	mQTLs with meta-analysis P < (0.05/10,213,925) from 66 types of metabolites (386,995)
Transcriptomics	eQTLs(227 muscle, 120 liver and 117 adipose)	eQTLs with meta-analysis (0.05) from 3 types of tissues (240,683)
Epigenomics	OCR (10)	Peak calling for muscle samples was performed using Genrich with -m 30, -j (ATAC-seq mode), -r (remove PCR duplicates), -e MT (to exclude mitochondrial chromosome), -q 0.05 (FDR-adjusted P-value) (495,903)
	HMRs (10)	chose a 10 kb window size with the default parameters (762,835)

The LD score indicates the linkage disequilibrium between pairwise variants in the surrounding 50-kb region. For the three quartiles, fourth quartile scores > third quartile > second quartile > first quartile. NA indicates sample from public data