List Of All Known Regulatory Regions In Human Genome

Question

[Abdel]

Hi all,

Is there a way to get a list of the start and end base pair positions of all known regulatory sequences (cis, trans, promotors, etc) in the human genome? Many thanks in advance!

Answer 1

[Pierre Lindenbaum]

see the ENCODE project: http://genome.ucsc.edu/ENCODE/downloads.html ( good luck...)

Answer 2

[Kevin]

If you define X kb upstream of a gene to be a promoter, you can get this using the UCSC table browser as follows: Hg19 Promoters .Bed File

Answer 3

[2184687-1231-83-]

Either the ENCODE project or any other FAIRE-seq (http://en.wikipedia.org/wiki/FAIRE-Seq) public dataset deeply sampled on human tissues would be a good approximation. The current estimates is that 20% of the human genome is doing something (TM).

Answer 4

[Casey Bergman]

All Ensembl regulatory features can be obtained from biomart using this query.

[Abdel]

Thanks! So what's the difference between all these and the ones from ENCODE?

[Casey Bergman]

Email the Ensembl helpdesk if the following page does not answer your question: http://www.ensembl.org/info/docs/funcgen/index.html