Single nucleotide polymorphisms (SNPs) and small insertions/deletions (2-50bp) in genomic regulatory regions may impact function, and although widespread, they are largely unexplored in livestock. Over 113 million candidate functional variants were annotated using data from nearly 900 epigenomic datasets across 10 species. The function of variants depends heavily on their influence on regulatory elements. We identified the primary tissues in which functional variants are active by analyzing regulatory signals co-located with these variants, leading to the construction of a comprehensive cis-regulatory element (CRE) map for the pig genomeacross ten spieces. We also identified topologically associating domains (TADs) and loops from 56 Hi-C datasets, using them to associate SNPs with genes. Further integration of single-cell RNA-seq data revealed that different trait-related variants were enriched in different cell types. Therefore, we developed the Integrated Functional Mutation (IFmut) platform(http://www.ifmutants.com:8212) for users to effortlessly navigate and uncover potential function of variants. Our work offers a powerful and flexible platform for the study of genomic variation in farm animals, setting a new benchmark in livestock research and breeding strategies.
 

SNP, cis-regulatory element, Hi-C,single-cell RNA-seq, database