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Numerous genetic variations have been found to be associated with human diseases. A significant portion of these affect drug response by changing protein structure and function. Therefore, it is crucial to understand the trilateral relationship among genomic variations, diseases, and drugs. We present VnD (Variations and Drugs), a consolidated database containing information on diseases, disease and drug related genes, genetic variations, protein structures, and drug information. VnD was built in three steps. First, we systematically integrated various resources to deduce catalogs of disease-related genes, single nucleotide polymorphisms (SNPs), protein mutations, and relevant drugs. VnD contains 137,195 disease-related gene records (13,940 distinct genes) and 16,586 genetic variation records (1,790 distinct variations). Next, we carried out structural modeling and docking simulations for wild-type and mutant proteins to examine the structural and functional consequences of non-synonymous SNPs on drug-related genes. Conformational changes in 590 wild-type and 4,437 mutant proteins from drug-related genes were included in our database. Finally, we investigated the structural and biochemical properties relevant to drug binding such as the distribution of SNPs in proximal protein pockets, thermo-chemical stability, interactions with drugs, and physico-chemical properties. The VnD database is a useful platform for researchers studying the mechanisms underlying the association among genetic variations, diseases, and drugs