Fig. 2

eQTLs in three tissues. a Manhattan plot showing the nominal P-value (y-axis) for all cis-eQTLs in muscle. b The TPM normalized expression of LEAP2 with three genotypes. c Dot plot showing the locations, P-value, and effect sizes for all significant trans-eQTL in muscle. Variants and gene positions are shown on the x-axis and y-axis, respectively. Each dot was a significant trans-eQTLs (FDR < 0.05). The size of each dot represents the −log10 scaled P-values. The color of each dot represents the direction of the slope effect. d Distribution of cis-eQTLs around TSS. All SNP-gene pairs indicate all tested SNP-gene pairs. Non-eQTL indicates the top associated SNP for non-eGenes. e The distance of the most significant eVariant to the TSS of eGene in muscle. The primary signals (golden) and the secondary signals (blue) relative to TSS are shown using a point plot (left) and their absolute distances compare shown in the box plot (right). The Wilcoxon test is used to compute significance. f The absolute allelic fold change distribution for cis-eQTLs in three tissues. g The proportion and enrichment of cis-eQTLs in genome location. The enrichment factors are based on the number of cis-eQTLs in each region category divided by the expected number. h Enrichment of eQTLs in five chromatin states predicted from a tissue-matched cattle dataset. The x-axis represents the enriched fold