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Welcome to PheGenI

The Phenotype-Genotype Integrator (PheGenI), merges NHGRI genome-wide association study (GWAS) catalog data with several databases housed at the National Center for Biotechnology Information (NCBI), including Gene, dbGaP, OMIM, eQTL and dbSNP.  This phenotype-oriented resource, intended for clinicians and epidemiologists interested in following up results from GWAS, can facilitate prioritization of variants to follow up, study design considerations, and generation of biological hypotheses.  Users can search based on chromosomal location, gene, SNP, or phenotype and view and download results including annotated tables of SNPs, genes and association results, a dynamic genomic sequence viewer, and gene expression data. PheGenI is still under active development.  Currently, the phenotype search terms are based on MeSH and will be enhanced with additional options in the future. Download all association results or enter search criteria below.

Search Criteria

Phenotype SelectionGet information.

Traits:
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Click to remove item, hold the shift key down to remove all items
Click to remove item, hold the shift key down to remove all items
Click to remove item, hold the shift key down to remove all items
Click to remove item, hold the shift key down to remove all items
< 1 x 10 - Source:

Genotype SelectionGet information.

Chromosome:
(from:to)
SNP Functional Class
ClearInvert
Enter search criteria using the controls below.  Use the label or arrow on the left to hide / show any section.  Small arrows at the far right side of each section heading to move the section above or below an adjacent section.
Select broad trait category to limit the items shown in the trait selection.
Select trait for search.  Selection of a trait will limit the trait categories shown above.
Data shown are compiled from both NHGRI GWAS Catalog (Source = NHGRI) and from most significant hits across analyses submitted to dbGaP.
Data shown are selected columns matching search criteria, taken directly from NCBI Gene.
Data shown are selected columns matching search criteria, taken directly from Entrez dbSNP.
Data shown are selected columns matching search criteria, taken directly from NCBI’s GTEx database and browser.  This database aims to provide a central resource to archive and display associations between genetic variation and high-throughput molecular-level phenotypes.  This effort originated with the NIH GTEx roadmap project; however the scope of this resource will be extended to include any available genotype/molecular phenotype datasets.
Data shown are molecular QTL datasets extracted from the NCBI molQTL resource (coming soon) by matching search criteria.
Data shown are selected dbGaP study information related to the trait information in the Association Results.  Each study name is hyperlinked to the corresponding dbGaP study page where the user can apply for authorized access to individual-level data.
The ideogram view is shown for all genomic locations specified in the search which span regions with SNP and Gene Results.

The orientation can be selected as vertical, horizontal, or the default can be used.  The default is horizontal if one chromosome is displayed and vertical otherwise.

The user has the option of including SNPs and or Genes in the display.  If the search criteria include a location it can also be displayed.

The 'Display' option is either the current subset of the SNPs and Genes displayed on the page (e.g., 1 - 50 of 75) or those from all Association Results (e.g., all 75) including those that do not appear in the current page of the Association Results table.  Due to the potential volume of data, the latter option is available only if a phenotype trait was selected in the initial search.