Many diseases are associated with single-nucleotide polymorphisms that affect critical regions of proteins as binding sites or post-translational modifications. Therefore, analysing genomic variants with structural and molecular biology data is a powerful framework in order to elucidate the potential causes of such diseases. Anew version of our web framework 3DBIONOTES is presented. This version offers new tools to analyse and visualize protein annotations and genomic variants, including a contingency analysis of variants and amino acid features by means of a Fisher’s exact test, the integration of a gene annotation viewer to highlight protein features on gene sequences, and a protein–protein interaction viewer to display protein annotations at the network level.