Understanding functional consequences of genetic variants on the transcriptome of livestock is essential for interpreting the molecular mechanisms underlying traits of economic value, and for improving the rate of genetic gain through artificial selection. Here, we build a cattle Genotype-Tissue Expression atlas (cGTEx) for the research community based on 11,642 RNA-seq publicly available datasets (by July, 2019), representing over 100 tissues/cell types among over 40 breeds. We describe the landscape of transcriptome across tissues and report thousands of cis- and trans- genetic variants (QTLs) associated with gene expression and alternative splicing for 24 major tissues in cattle. Additionally, we detect 496 gene-tissue pairs significantly associated with 43 economically important traits in cattle via a large transcriptome-wide association study (TWAS). All the genome annotation files are based on ARS-UCD1.2 (Ensembl 96 version). The cGTEx Portal allows researchers to query gene expression, alternative splicing and QTLs across tissues in an easy and uniform way, which can serve as a primary source of reference for cattle genomics, cattle breeding, adaptive evolution, comparative genomics, and veterinary medicine.