Phenotype Data

Diseases and traits that are associated with the variant of interest are shown on this page.

The different sources of this data can be found in the second column of the table and some examples are listed below:

• COSMIC http://www.sanger.ac.uk/genetics/CGP/cosmic/
• ClinVar (Variants of clinical significance from ClinVar): http://www.ncbi.nlm.nih.gov/clinvar/
• dbGaP (The database of Genotypes and Phenotypes): http://www.ncbi.nlm.nih.gov/gap
• EGA http://www.ebi.ac.uk/ega
• GIANT (Genetic Investigation of ANthropometric Traits ): http://www.broadinstitute.org/collaboration/giant/index.php/Main_Page
• HGMD-Public http://www.hgmd.cf.ac.uk/ac/index.php
• MAGIC (Meta-Analyses of Glucose and Insulin-related traits Consortium): http://www.magicinvestigators.org/
• NHGRI-EBI GWAS catalog http://www.ebi.ac.uk/gwas/

Ontology mappings and accession terms related to phenotypes associated with the vaRIANT of interest are also included in the table. Ontology annotations of human phenotypes are imported from EFO, Human Phenotype Ontology and Orphanet. 

The reported gene comes directly from the specific study (linked in the second column), as do the associated allele, p value, odds ratio and beta coefficient (if available). These are genes that were reported in the paper as being associated with this GWAS variant, and may not correspond to the genes reported on the Genes and Regulation page for the variant. The associated allele is also that reported in the paper, and may be the positive or negative strand allele (the alleles shown in Ensembl are always the positive strand alleles).

The statistics that may be displayed are:

Odds ratio: The odds of having the phenotype if you have the associated allele or genotype, compared to the odds of having the phenotype in the general population.

P-value: The probability that the association (odds ratio) between the locus and the phenotype is due to chance, usually calculated through a chi-squared test.

Beta coefficient: A measure of the standard error.

It is recommended that you read the publications to determine exactly how individual statistics are calculated.

Click on the associated allele to see the frequency of that allele in 1000 Genomes populations.

It is possible to retrieve the list of variations associated to the phenotypes in BioMart or their locations can be viewed on the karyotype.

Check the Variation - Data sources for a full list of sources of variation data currently available in Ensembl.