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Next generation sequencing, genome editing, deep mutational scans, and single cell biology are opening up unprecedented opportunities to understand how genetic variation alters molecular mechanisms to cause phenotypic variation amongst individuals, including quantitative traits and human disease. This first EMBO|EMBL Symposium on systems genetics will focus on the central questions of when and how do changes in genotype result in changes in phenotype? This meeting will bring together groups using experimental, statistical and mechanistic modelling approaches to address these questions at different scales and in diverse model systems, including for human disease.