Variant
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.
| Column | Description |
|---|---|
| Cell Type | Cell type in which the enhancer is predicted to regulate the gene |
| Target Gene | Gene predicted to be regulated by the enhancer |
| Score | Strength of the prediction (range: 0 to 1, higher indicates a more confident prediction) |
| Dataset | Source dataset |
| Model | Predictive model. Currently: ENCODE-rE2G |
| Variant-Gene Distance | Genomic 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.
Variants in Linkage Disequilibrium Table
This table displays information about variants that are in linkage disequilibrium (LD) with the current variant.
| Column | Description |
|---|---|
| rsID | The reference SNP ID (click for more details) |
| LD (r²) and LD (D’) | Measures of linkage disequilibrium |
| Cell Types w/ pred. EG link | Cell types with predicted enhancer-gene links |
| Genes w/ pred. EG link | Genes with predicted enhancer-gene links |
| Ancestry | The population ancestry for the LD information |
| Most Severe Consequence | The predicted functional impact |
You can filter this table by ancestry using the dropdown menu above the table.
GWAS Association Table
This table shows phenotypes (traits or diseases) associated with the variant through genome-wide association studies (GWAS).
| Column | Description |
|---|---|
| Phenotype Term | The associated trait or disease |
| Study Details | Information about the study (ID, name, author, etc.) |
| p-value | The statistical significance of the association |
| Beta | The effect size and direction |
Coding Variant Prediction Table
If the variant affects a protein-coding region, this table provides predictions about its impact on protein function.
| Column | Description |
|---|---|
| Gene and Transcript Information | Details about the affected gene and transcript |
| Protein Change | How the variant changes the protein sequence |
| Prediction Scores | Various 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.