PhenoScanner V2 is an updated version of the PhenoScanner database, which facilitates 'phenome scans' by cross-referencing genetic variants with various phenotypes. This tool has been significantly expanded to include over 150 million genetic variants and more than 65 billion associations with diseases, traits, gene expression, metabolite levels, protein levels, and epigenetic markers. The new features include enhanced search options for genes, genomic regions, and phenotypes, as well as linkage disequilibrium (LD) statistics from the 1000 Genomes project. The database is curated from over 5000 genetic association datasets and uses the Variant Effect Predictor and Experimental Factor Ontology for variant annotation and phenotype mapping. The updated tool is available at www.phenoscaner.medschl.cam.ac.uk and can be accessed via a web interface and API. The expanded database and additional functionalities have been demonstrated to significantly enhance the identification of genetic associations with phenotypes, as shown in a case study using the variant rs10840293 and the gene SWAP70.PhenoScanner V2 is an updated version of the PhenoScanner database, which facilitates 'phenome scans' by cross-referencing genetic variants with various phenotypes. This tool has been significantly expanded to include over 150 million genetic variants and more than 65 billion associations with diseases, traits, gene expression, metabolite levels, protein levels, and epigenetic markers. The new features include enhanced search options for genes, genomic regions, and phenotypes, as well as linkage disequilibrium (LD) statistics from the 1000 Genomes project. The database is curated from over 5000 genetic association datasets and uses the Variant Effect Predictor and Experimental Factor Ontology for variant annotation and phenotype mapping. The updated tool is available at www.phenoscaner.medschl.cam.ac.uk and can be accessed via a web interface and API. The expanded database and additional functionalities have been demonstrated to significantly enhance the identification of genetic associations with phenotypes, as shown in a case study using the variant rs10840293 and the gene SWAP70.