(A) A Schematic overview of the GC gene structure and position of the GC CNV. Our data detected two GC transcripts, where the canonical form account the majority of the expression (98%) and an alternative form only counting for minor expression (2%). (B) eQTL was mapped for the genes located in a 2-Mb bin (BTA6:87.68–89.68). Of the 13 genes annotated in this bin, GC showed predominantly high expression (5,000 TPM <), whereas the rest were lowly expressed or not expressed at all. The eQTL were mapped for GC and SLC4A4 . (C) CM resistance fine-mapping results were shown for the 2-Mb bin, where eQTL was mapped. The color scale indicates the degree of pair-wise LD (r 2 ) between the GC CNV and other SNPs. Annotation of genes in this region is drawn as black bars. Six genes on the left part are AMBN , JCHAIN , RUFY3 , GRSF1 , MOB1B , and DCK . (D) eQTL mapping results for GC (canonical transcript). (E) P-values obtained from CM resistance fine-mapping and GC eQTL mapping (canonical transcript) were correlated. The GC CNV is located in the right upper corner (ρ = 0.68), showing that it is significant for both fine-mapping and eQTL mapping. (F) The box plot shows altered GC (canonical transcript) expression depending on GC CNV genotypes. (G) eQTL mapping result for GC (alternative transcript). (H) P-values obtained from CM resistance GWAS and GC eQTL mapping (alternative transcript) were correlated. The GC CNV is located in the right upper corner (ρ = 0.74), showing that it is significant for both fine-mapping and eQTL mapping. (I) The box plot shows altered GC (alternative transcript) expression depending on GC CNV genotypes. Panels C-E, G, H were made with LocusCompare programme [ 99 ].