PhenoScanner V2 is an updated version of the online tool for searching human genotype-phenotype associations. It includes over 150 million genetic variants and more than 65 billion associations with diseases, traits, gene expression, metabolite and protein levels, and epigenetic markers. The tool allows users to search by genes, genomic regions, phenotypes, and genetic variants. All variants are annotated using the Variant Effect Predictor, and phenotypes are mapped to Experimental Factor Ontology terms. Linkage disequilibrium statistics from the 1000 Genomes project can be used to search for phenotype associations with proxy variants. PhenoScanner V2 has a new web interface and API, allowing users to search for genotype-phenotype associations in R or from a terminal. The database includes results for diseases and traits (30 billion associations), gene expression (84 million associations), protein levels (35 billion associations), metabolite levels (3 billion associations), and epigenetic markers (13 million associations). The tool enables users to search for genetic variants, genes, genomic regions, or traits and provides results with P-values. PhenoScanner V2 has expanded the scope of PhenoScanner V1 in both scale and phenotypic breadth, with additional annotation and functionality. The database can now be searched for genes, genomic regions, and traits, while variant annotation, phenotype ontology mappings, and LD statistics from a wider range of ethnic groups have been incorporated to enhance utility and interpretation. Funding for this work was provided by various organizations including the UK Medical Research Council, the British Heart Foundation, Pfizer, the European Research Council, and the European Commission Framework Programme 7.PhenoScanner V2 is an updated version of the online tool for searching human genotype-phenotype associations. It includes over 150 million genetic variants and more than 65 billion associations with diseases, traits, gene expression, metabolite and protein levels, and epigenetic markers. The tool allows users to search by genes, genomic regions, phenotypes, and genetic variants. All variants are annotated using the Variant Effect Predictor, and phenotypes are mapped to Experimental Factor Ontology terms. Linkage disequilibrium statistics from the 1000 Genomes project can be used to search for phenotype associations with proxy variants. PhenoScanner V2 has a new web interface and API, allowing users to search for genotype-phenotype associations in R or from a terminal. The database includes results for diseases and traits (30 billion associations), gene expression (84 million associations), protein levels (35 billion associations), metabolite levels (3 billion associations), and epigenetic markers (13 million associations). The tool enables users to search for genetic variants, genes, genomic regions, or traits and provides results with P-values. PhenoScanner V2 has expanded the scope of PhenoScanner V1 in both scale and phenotypic breadth, with additional annotation and functionality. The database can now be searched for genes, genomic regions, and traits, while variant annotation, phenotype ontology mappings, and LD statistics from a wider range of ethnic groups have been incorporated to enhance utility and interpretation. Funding for this work was provided by various organizations including the UK Medical Research Council, the British Heart Foundation, Pfizer, the European Research Council, and the European Commission Framework Programme 7.