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  Sequence and Annotation Downloads

This page contains sequence and annotation data downloads for the ENCODE project. Table downloads are also available from selected human assembly directories (hg*) on the Genome Browser FTP server.

To view the current descriptions and formats of the tables in the annotation database, use the "describe table schema" button in the Table Browser.

  Terms of Use

All of the tables in the Genome Browser are freely usable for any purpose except as indicated in the README.txt files in the download directories. To view restrictions specific to a particular assembly, click on the corresponding download link below and scroll to the bottom of the page. This data was contributed by many researchers, as listed on the Genome Browser credits page. Please acknowledge the contributor(s) of the data you use.

Note that specific restrictions on the use of the ENCODE data are in place, and can be accessed here.

  Downloads of the Human Genome and Annotations
  Mar. 2006 (UCSC hg18, NCBI Build 36) - ENCODE Reference Assembly May 2004 (UCSC hg17, NCBI Build 35) - Previous ENCODE Reference Assembly Jul. 2003 (UCSC hg16, NCBI Build 34) - First ENCODE Reference Assembly

Older assemblies (hg12, hg13, hg15)

  LiftOver Files (over.chain)
  • hgLiftOver tool (web-based version)
  • LiftOver tool (downloadable Linux binary executable)
  • hg17 to hg18 (NCBI Build 35, May 2004 lifted to NCBI Build 36, Mar. 2006)
  • hg16 to hg17 (NCBI Build 34, Jul. 2003 lifted to NCBI Build 35, May 2004)
  • hg15 to hg16 (NCBI Build 33, Apr. 2003 lifted to NCBI Build 34, Jul. 2003)
  • hg13 to hg16 (NCBI Build 31, Nov. 2002 lifted to NCBI Build 34, Jul. 2003)
  • hg12 to hg16 (NCBI Build 30, Jun. 2002 lifted to NCBI Build 34, Jul. 2003)