This study reports the first uniformly processed RNA-seq data from multiple human populations, providing a comprehensive analysis of transcriptome variation and its genetic causes. By sequencing and analyzing mRNA and miRNA from lymphoblastoid cell lines of 462 individuals from the 1000 Genomes Project, the authors discovered widespread genetic variation affecting gene regulation, with transcript structure and expression level variation being equally common but genetically largely independent. The characterization of causal regulatory variants sheds light on cellular mechanisms of regulatory and loss-of-function variation, allowing the inference of putative causal variants for dozens of disease-associated loci. The study provides a deep understanding of the cellular mechanisms of transcriptome variation and the landscape of functional variants in the human genome.This study reports the first uniformly processed RNA-seq data from multiple human populations, providing a comprehensive analysis of transcriptome variation and its genetic causes. By sequencing and analyzing mRNA and miRNA from lymphoblastoid cell lines of 462 individuals from the 1000 Genomes Project, the authors discovered widespread genetic variation affecting gene regulation, with transcript structure and expression level variation being equally common but genetically largely independent. The characterization of causal regulatory variants sheds light on cellular mechanisms of regulatory and loss-of-function variation, allowing the inference of putative causal variants for dozens of disease-associated loci. The study provides a deep understanding of the cellular mechanisms of transcriptome variation and the landscape of functional variants in the human genome.