> ## Documentation Index > Fetch the complete documentation index at: https://docs.catalog.igvf.org/llms.txt > Use this file to discover all available pages before exploring further. # Region ## Overview The IGVF Catalog contains genomic elements, which are potential functional regions for regulating gene expression. These elements are identified/tested by functional assays (e.g., MPRA), association studies (e.g., caQTLs), and computational predictions (e.g., the [ENCODE-rE2G model](https://www.biorxiv.org/content/10.1101/2023.11.09.563812v1.full)). Data sources include: * [ENCODE Candidate Cis-Regulatory Elements (cCREs)](https://doi.org/10.1038/s41586-020-2493-4): A unified set of genomic elements predicted to have regulatory potential based on a combination of experimental data (e.g., ChIP-seq, DNase-seq) from the ENCODE project. Additional genomic elements are added when studied in specific contexts, for example accessible elements used in predictive modeels or elements tested in an MPRA experiment or CRISPR screen ## Coding Variants ### Genomic Elements-Genes Edges | Source | Class | Edge Description | Datasets | | ------ | ------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | ENCODE | prediction | Biosample specific enhancer-gene predictions using [rE2G pipeline](https://www.encodeproject.org/pipelines/ENCPL835OUC/) | [ENCODE-rE2G](https://www.encodeproject.org/search/?type=Annotation\&status=released\&annotation_type=element+gene+regulatory+interaction+predictions\&lab.title=Jesse+Engreitz%2C+Stanford) | | IGVF | observed data | CRISPRa and CRISPRi Perturb-seq integrating a guide (sgRNA) library targeting transcription start sites in 24 genes in CD8-positive, alpha-beta memory T primary cells | [IGVF Perturb-seq assays](https://data.igvf.org/search/?type=AnalysisSet\&status=released\&preferred_assay_titles=Perturb-seq\&lab.title=Charles+Gersbach%2C+Duke\&collections=IGVF_catalog_v1.0) | | IGVF | observed data | CRISPRi CRISPRa CRISPRko FACS screen of CCR7 and IL7R inCD8-positive, alpha-beta memory T primary cells | [IGVF CRISPR FACS screen](https://data.igvf.org/search/?type=AnalysisSet\&status=released\&preferred_assay_titles=CRISPR+FACS+screen\&lab.title=Charles+Gersbach%2C+Duke\&collections=IGVF_catalog_v1.0) | ## Gene Regulation ### Genomic Elements-Biosamples Edges | Source | Class | Edge Description | Datasets | | ------ | ------------- | ------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | | ENCODE | observed data | lentiMPRA testing potential HepG2, K562, and WTC11 enhancers and promoters of all protein-coding genes. | [ENCODE lentiMPRA](https://www.encodeproject.org/search/?type=FunctionalCharacterizationExperiment\&accession=ENCSR405QCT\&accession=ENCSR203UFY\&accession=ENCSR336MKI) | | IGVF | observed data | lentiMPRA in 5 biosamples measuring effect of element (and variants) on gene expression | [IGVF lentiMPRA](https://data.igvf.org/search/?type=AnalysisSet\&status=released\&preferred_assay_titles=lentiMPRA\&collections=IGVF_catalog_v1.0) | ### Variants-Genomic Elements Edges (also on variants page) * External caQTL studies: variants associated with genomic elements function from external studies ([PMID:34038741](https://pubmed.ncbi.nlm.nih.gov/34038741/), [PMID:34017130](https://pubmed.ncbi.nlm.nih.gov/34017130/)) and [AFGR](https://github.com/smontgomlab/AFGR?tab=readme-ov-file)(African Functional Genomics Resource) * IGVF BlueSTARR: computational model predicts variants affecting the regulatory function in ENCODE cCREs (Candidate Cis-Regulatory Elements) * IGVF MPRA Table Columns: | Column | Description | | -------------------------------- | ------------------------------------------------------------------------- | | Region | Genomic coordinates of the regulatory region (clickable for more details) | | Biochemical Activity | The type of biochemical activity in this region | | Biochemical Activity Description | Detailed description of the biochemical activity | | Type | Classification of the regulatory region | | Source | Origin of the data | | Source URL | Link to the original data source (clickable) | Interacting with the Table: * Click on column headers to sort the table by that column * Use the search box above the table to filter results * Adjust the number of rows displayed using the dropdown menu * Navigate between pages using the "Previous" and "Next" buttons ### Biosample Table The Biosample Table provides information about biological samples associated with the regulatory regions in your selected genomic coordinates. Table Columns: | Column | Description | | ------------------------------------------ | ------------------------------------------------------------------------ | | Activity Score | Numerical score indicating the level of activity (higher is more active) | | Source | Origin of the biosample data (clickable link) | | Chromosome, Region Start, Region End | Location of the associated regulatory region | | Region Name, Region Type | Identifiers for the regulatory region | | Biochemical Activity, Activity Description | Details about the biochemical activity in the region | | Biosample Name | Name of the biological sample | | Term ID | Unique identifier for the biosample | | Description | Detailed description of the biosample | | Biosample Source | Origin of the biosample | | Subontology | Subclassification of the biosample, if applicable | ### Enhancer-Gene Prediction(s) This table reports whether the query region contains predicted enhancers from the ENCODE-rE2G model, and their target genes and cell types. Each row reports one predicted enhancer, 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](https://www.biorxiv.org/content/10.1101/2023.11.09.563812v1.full)) The table is initially sorted by Score in descending order, showing the strongest predictions first.