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Fig. 2 | BMC Genomics

Fig. 2

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

Fig. 2

GWAS results for tenderness (MQLDPF) and gene expression results, using RNA-Seq meta-analyses of all datasets, within 50 kb of calpastatin gene (CAST). The Manhattan plots show the GWAS results for MQLDPF in grey. The common GWAS suggestive line at p < 10− 5 and the genome-wide threshold line at p < 5 × 10− 8 are shown in blue and red, respectively. The dark shaded box indicates the location of CAST and light shaded boxes show 50 kb upstream and downstream of the gene. 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 calpastatin gene significantly associated with MQLDPF (p < 0.001) are in blue. The SNP significantly associated with expression of the gene (p < 0.001) as detected by ASE (top), local eQTL mapping (middle) and meta-analysis of ASE and local eQTL (bottom) are in red. Where the same dSNP was tested for multiple tSNP, the lowest p-value for each dSNP is shown in the graphs. Although ASE and local eQTL mapping are different measurements they show similar results

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