Supporting data for "Identification of transcriptional regulatory variants in pig duodenum, liver and muscle tissues"

In humans and livestock species, genome-wide association studies (GWAS) have been applied to study the association between variants distributed across the genome and a phenotype of interest. To discover genetic polymorphisms affecting the duodenum, liver, and muscle transcriptomes of 300 pigs from three different breeds (Duroc, Landrace and Large White), we performed expression GWAS between 25,315,878 polymorphisms and the expression of 13,891 genes in duodenum, 12,748 genes in liver, and 11,617 genes in muscle. <br>More than 9.68×10¹¹ association tests were performed, yielding 14,096,080 significantly associated variants, which were grouped in 26,414 expression quantitative trait locus (eQTL) regions. Over 56% of the variants were within 1Mb of their associated gene. In addition to the 100kb region upstream of the transcription start site, we identified the importance of the 100kb region downstream of the 3UTR for gene regulation, as most of the <em>cis</em>-regulatory variants were located within these two regions. We also observed 39,874 hotspot regulatory polymorphisms associated with the expression of 10 or more genes that could modify the protein structure or the expression of a regulator gene. In addition, two motifs (5-GATCCNGYGTTGCYG-3 and a poly(A) sequence) were enriched across the three tissues within the neighbouring sequences of the most significant SNPs in each <em>cis</em>-eQTL region. <br>The 14 million significant associations obtained in this study are publicly available and have enabled the identification of expression-associated <em>cis</em>-, <em>trans</em>- and hotspot regulatory variants within and across tissues, thus shedding light on the molecular mechanisms of regulatory variations that shape end-trait phenotypes.