The integration of genomics, proteomics and phenotypic traits across genetically diverse populations is a powerful approach to discover novel biological regulators. The increasing volume of complex data require new and easy-to-use tools accessible to a variety of scientists for the discovery and visualization of functionally relevant associations. To meet this requirement, we developed CoffeeProt, an open-source tool that analyzes genetic variants associated to protein networks and phenotypic traits. CoffeeProt uses proteomics data to perform correlation network analysis and annotates protein-protein interactions, subcellular localizations and drug associations. It then integrates genetic and phenotypic associations along with variant effect predictions. We demonstrate its utility with a step-by-step tutorial of the workflow in the analysis of mouse data, highlighting the rapid identification of genetic variants associated with druggable proteins and clinical traits. We expect that CoffeeProt will serve the proteomics and systems genetics communities, leading to the discovery of novel biologically relevant associations. CoffeeProt is available at www.coffeeprot.com.