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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.

< 1 x 10 - Source:

Genotype SelectionGet information.

Gene names or IDs:
SNP rs numbers:
SNP Functional Class
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.
Enter the name of any trait or disease and a window will appear with a list of suggestions.  Currently, phenotypes are matched to exact MeSH terms; parent, child and synonyms are not indexed.  If you wish to narrow your search by category, click on the Browse... button.  When more than one trait is selected, the search results will include records that match any of the selected traits.  You may also limit the P-value for the Association Results and eQTL data to be less than the specified value.
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.
Genetic location may be specified in one of three ways:
  1. Location: chromosome and range (position on chromosome)
    Range is specified as two numbers in multiple formats by a space, hyphen, or comma.  The following examples are equivalent:
    1000K 10000K
  2. Gene: One or more gene symbols or NCBI Gene IDs separated by spaces, commas, or on separate lines.
  3. SNP: One or more dbSNP rs numbers separated by spaces, commas, or on separate lines.  The 'rs' prefix is optional.

You may optionally select one or more SNP functional classes.  If none are selected, then all functional classes are included including 'intergenic.'
This entire section is optional if a category and/or trait are selected in the phenotype selection.
Available Traits:   ClearInvert
Selected Traits: