Dataset: Locations of regulatory sequences in the human genome? I am looking for the positions of annotated regulatory sequences (promoters, enhancers and suppressors) in the human genome.

I looked at Ensembl regulatory Build and PAZAR but I am not used to look for datasets and I failed to find what I was looking for.

Can you help to find annotated regulatory sequences (start and end positions) in the human genome?
This can be done quite easily using Ensebl's BioMart.


Choose the Ensembl Regulation database:

 
Select the "Human Regulatory Features" dataset:


That's basically it right there, just click on "Results":


Export to file and click "Go":




This will download a file called mart_export.txt which looks like this (I chose TSV for tab separated values):

$ head mart_export.txt 
Chromosome/scaffold name    Start (bp)  End (bp)    Feature type
18  76429380    76430144    Open chromatin
8   66405962    66406502    Open chromatin
4   61184401    61184600    CTCF Binding Site
X   40733600    40737000    Promoter
5   97407001    97407200    CTCF Binding Site
X   73946201    73946600    Promoter Flanking Region
15  19948201    19949200    CTCF Binding Site
5   11302601    11303143    Open chromatin
2   208407801   208408000   CTCF Binding Site


As you can see the format is pretty straightforward. The first column has the chromosome or scaffold name (it should always be a chromosome for human), the second and third are the star and end positions and the last field is the type of region. 

You can also choose to limit by region type by choosing a filter (click the "Filters" link) in BioMart before downloading or by simply parsing the file once you've downloaded it.