Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2019 Nov 1;35(22):4851-4853.
doi: 10.1093/bioinformatics/btz469.

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

Mihir A Kamat  1 , James A Blackshaw  1 , Robin Young  1 , Praveen Surendran  1 , Stephen Burgess  1   2 , John Danesh  1   3   4 , Adam S Butterworth  1   4 , James R Staley  1   5
Affiliations

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

Mihir A Kamat et al. Bioinformatics. .

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 genetic variants are cross-referenced for association with many phenotypes of different types. Here we present a major update of PhenoScanner ('PhenoScanner V2'), including over 150 million genetic variants and more than 65 billion associations (compared to 350 million associations in PhenoScanner V1) with diseases and traits, gene expression, metabolite and protein levels, and epigenetic markers. The query options have been extended to include searches by genes, genomic regions and phenotypes, as well as for genetic variants. All variants are positionally annotated using the Variant Effect Predictor and the 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.

Availability and implementation: PhenoScanner V2 is available at www.phenoscanner.medschl.cam.ac.uk.

PubMed Disclaimer

References

    1. 1000 Genomes Project Consortium et al. (2015) A global reference for human genetic variation. Nature, 526, 68–74. - PMC - PubMed
    1. Astle W.J. et al. (2016) The allelic landscape of human blood cell trait variation and links to common complex disease. Cell, 167, 1415–1429. - PMC - PubMed
    1. GTEx Consortium et al. (2017) Genetic effects on gene expression across human tissues. Nature, 550, 204–213. - PMC - PubMed
    1. Harrow J. et al. (2012) GENCODE: the reference human genome annotation for the encode project. Genome Res., 22, 1760–1774. - PMC - PubMed
    1. MacArthur J. et al. (2017) The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog). Nucleic Acids Res., 45, D896–D901. - PMC - PubMed

Publication types