Fig. 4: Functional regulatory features of PBMCs- and Neu-specific molQTLs.

A Numbers of overlapping and cell type-specific molGenes (eGenes, sGenes, and apaGenes) identified in PBMCs and Neu. B Functional enrichment analysis results of target genes regulated by PBMCs- and Neu-specific molQTLs. C Enrichment analysis for immune trait-associated eGenes in PBMCs and Neu. Significant eGenes were identified by overlapping results from the linear regression model and WGCNA (odds ratios calculated using Fisher’s exact test; * indicates significant enrichment: P < 0.05). D Cell type-specific regulatory networks linking phenotype-associated eQTLs, eGenes, and pathways. Representative SNPs (rsIDs) are shown, prioritized for their regulation of genes significantly associated with porcine neutrophil percentage (Neu%). Pathways are derived from enrichment analysis of WGCNA module genes. Arrow direction indicates the regulatory relationship; SNP colors denote the direction of effect (red: positive, green: negative). Genes are grouped by pathway (black circles: innate immune response; light brown circles: IFN signaling pathway). E Identification and characterization of cyto-cis and cyto-trans genes (defined in main text) in PBMCs and Neu, along with their regulating eQTLs. The upper panel shows the proportion of cyto-cis eGenes associated with immune phenotypes in each cell type, and the lower panel shows the corresponding proportion for cyto-trans eGenes. Color intensity represents the proportion of phenotype-associated eGenes.