Functional genomics repository (FILER) is a functional genomics database developed by NIAGADS with the most comprehensive harmonized, extensible, indexed, searchable human functional genomics data collection across >20 data sources:

  • One place to access all data: query by tissue/cell type, biosample type, assay, data type, data collection
  • Useful for reproducible research
  • Integration with high-throughput genetic and genomic analysis workflows
  • Harmonized data, uniform, consistent data formats
Genomic Tracks
33.9 billion
Genomic intervals
7.2 trillion
Base pairs
Genomic coverage
648.03 GB
File size (compressed)

FILER Workflow

Getting Started

To get started, click on the Search to search by genomic coordinates, upload and analyze your own data, or click Browse to explore FILER functional genomics datasets and annotations. See Deploy to download and install FILER on a local server or cloud computing instance.

The Summary page provides an overview of FILER data contents by primary data sources, tissue and cell type categories, genomic feature type categories and experimental assays.

The About page provides details on FILER data source curation, data pre-processing and annotation.


Mar 13, 2024 FILER v1.4 update: cell type/tissue-related metadata has been updated for all FILER tracks FILER v1.4 GRCh38/hg38 metadata
Feb 09, 2023 FILER v1.1f update: metadata has been updated for ENCODE, EpiMap and FANTOM5 tracks FILER v1.1f GRCh38/hg38 metadata
Jan 20, 2023 FILER v1.1 update: ENCODE native GRCh38/hg38 data (33,708 tracks) has been released FILER v1.1 GRCh38/hg38 metadata
Aug 03, 2022 FILER v1.0.2 update: EpiMap GRCh38/hg38 and GRCh37/hg19 enhancer data tracks have been added FILER v1.0.2 metadata
April 16, 2022 FILER tutorial is now available.
Mar 22, 2022 FILER v1.0.1 update: FANTOM5 native GRCh38/hg38 enhancer data tracks have been added FILER v1.0.1 metadata
Feb 07, 2022 News article about FILER web server in PNGC Read here PNGC blog article
Jan 14, 2022 FILER paper has been published in NAR Genomics and Bioinformatics
Dec 13, 2022 FILER manuscript has been accepted for publication in NAR Genomics and Bioinformatics
Aug 11, 2021 FILER v1 code and scripts are now available at FILER repository
Jun 04, 2021 FILER pre-print is now available in bioRxiv at

Citation & data use

External data users may freely download, analyze and publish results based on any FILER data.

If you use FILER functional genomics database in your research, please cite:


Kuksa PP, Leung YY, Gangadharan P, Katanic Z, Kleidermacher L, Amlie-Wolf A, Lee C-Y, Qu L, Greenfest-Allen E, Valladares O, Wang L-S (2022) FILER: a framework for harmonizing and querying large-scale functional genomics knowledge. NAR Genomics Bioinformatics.

as well as the orginal publications producing the raw data and aknowledge the funding that they received (see also Data acknowledgements tab)


National Institute on Aging [U24-AG041689, U54-AG052427, U01-AG032984].