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Enhancer-Gene Model Prediction Table

This table shows which genes are predicted to be regulated by enhancers overlapping the query variant. Each row reports one predicted target gene and cell type.
ColumnDescription
Cell TypeCell type in which the enhancer is predicted to regulate the gene
Target GeneGene predicted to be regulated by the enhancer
ScoreStrength of the prediction (range: 0 to 1, higher indicates a more confident prediction)
DatasetSource dataset
ModelPredictive model. Currently: ENCODE-rE2G
Variant-Gene DistanceGenomic distance between the variant and gene body
Currently, this table includes predictions from the ENCODE-rE2G model across 1700+ ENCODE biosamples (see Gschwind et al. bioRxiv 2023) The table is initially sorted by Score in descending order, showing the strongest predictions first.

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Variants in Linkage Disequilibrium Table

This table displays information about variants that are in linkage disequilibrium (LD) with the current variant.
ColumnDescription
rsIDThe reference SNP ID (click for more details)
LD (r²) and LD (D’)Measures of linkage disequilibrium
Cell Types w/ pred. EG linkCell types with predicted enhancer-gene links
Genes w/ pred. EG linkGenes with predicted enhancer-gene links
AncestryThe population ancestry for the LD information
Most Severe ConsequenceThe predicted functional impact
You can filter this table by ancestry using the dropdown menu above the table.

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GWAS Association Table

This table shows phenotypes (traits or diseases) associated with the variant through genome-wide association studies (GWAS).
ColumnDescription
Phenotype TermThe associated trait or disease
Study DetailsInformation about the study (ID, name, author, etc.)
p-valueThe statistical significance of the association
BetaThe effect size and direction

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Coding Variant Prediction Table

If the variant affects a protein-coding region, this table provides predictions about its impact on protein function.
ColumnDescription
Gene and Transcript InformationDetails about the affected gene and transcript
Protein ChangeHow the variant changes the protein sequence
Prediction ScoresVarious tools’ predictions of the variant’s impact (higher scores generally indicate more severe impacts)
Each table can be sorted by clicking on the column headers. You can also use the search box above each table to filter the results.