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Fig. 3 | BMC Genomics

Fig. 3

From: Comparing allele specific expression and local expression quantitative trait loci and the influence of gene expression on complex trait variation in cattle

Fig. 3

The overlap between QTL and gene expression within 50 kb of calpain (CAPN1), leptin receptor transcript-like 1 gene (LEPROTL1) and ligand dependent nuclear receptor corepressor-like (LCORL) genes. The Manhattan plots show the GWAS results for MQLDPF (top), PW_HIP (middle) and the multi-trait test (bottom) in grey. The common GWAS suggestive line at 10− 5 and the genome-wide threshold line at 5 × 10− 5 are shown in blue and red, respectively. The dark shaded boxes and light shaded boxes indicate the location and 50 kb upstream and downstream of the genes. For ease of comparison, the common SNPs from both the GWAS and the gene expression study are plotted in each graph. The SNPs within 50 kb of CAPN1, LEPROTL1 and LCORL genes, tested in gene expression analyses and significant GWAS (p < 0.001) are in blue. The SNPs significantly influenced expression of CAPN1 and LEPROTL1 in ASE measurement, and LCORL in combined ASE and eQTL meta-analysis of all RNA-Seq datasets (p < 0.001) are shown in red

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