PhenoScanner V2: an expanded tool for searching human genotype–phenotype associations

• DOI: 10.1093/bioinformatics/btz469
• Publication Date: 2019-06-19T19:13:03Z
• Authors: Mihir A Kamat; James A Blackshaw; Robin Young; Praveen Surendran; Stephen Burgess; John Danesh; Adam S Butterworth; James R Staley
• Keywords: Phenome; Linkage Disequilibrium; Genetic Association; Genome-wide Association Study; Phenotypic trait

Abstract Summary PhenoScanner is a curated database of publicly available results from large-scale genetic association studies in humans. This online tool facilitates ‘phenome scans’, where variants are cross-referenced for with many phenotypes different types. Here we present major update (‘PhenoScanner V2’), including over 150 million and more than 65 billion associations (compared to 350 V1) diseases traits, gene expression, metabolite protein levels, epigenetic markers. The query options have been extended include searches by genes, genomic regions phenotypes, as well variants. All positionally annotated using the Variant Effect Predictor mapped Experimental Factor Ontology terms. Linkage disequilibrium statistics 1000 Genomes project can be used search phenotype proxy Availability implementation V2 at www.phenoscanner.medschl.cam.ac.uk.