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, GTEx 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.

Search Criteria

Phenotype Selection

< 1 x 10 -

Genotype Selection

Range (bps):
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.
Select any category to show all traits for that category and/or choose any Trait to show all categories for that trait.  Categories and traits are shown as valid MeSH terms matched by NCBI staff.  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 Entrez 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.
Ideogram view is shown for all genomic locations specified in the search which span regions with association results.

The sequence display is shown automatically if a single genomic location matches the search criteria and spans regions with association results.  If multiple regions match search criteria, the sequence display is shown after clicking on one of the ideogram labels.

In the sections with tabular data, if the number of records exceeds the size of the table and another page is selected, the genome view section is initially closed and can be opened by clicking on the arrow to the left of the section title.
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 Entrez 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.