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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?

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  • $\begingroup$ Nice to see you here! Could you clarify what type of regulatory sequences you'd want? All of them? Would you include promoters in that or only things like splicing enhancers/supressors? $\endgroup$
    – terdon ♦
    Jun 16, 2017 at 14:40
  • $\begingroup$ Yes, both promoters, enhancers and suppressors (TBH, I did not think of promoter when asking my question but I'd like to consider them as well). Annotation on what type of sequence (promoter, enhancer/supressor) it is would be great. Post edited to add this info. Thanks @terdon $\endgroup$
    – Remi.b
    Jun 16, 2017 at 14:42

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This can be done quite easily using Ensebl's BioMart.

  1. Choose the Ensembl Regulation database:

    Ensembl screenshot

  2. Select the "Human Regulatory Features" dataset:

    human regulatory features

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

    results link

  4. Export to file and click "Go":

    GO link

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.

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  • $\begingroup$ Amazing! The Images link are broken but your step by steps explanations were very easy to follow even without images. Thanks a lot @terdon! +1 $\endgroup$
    – Remi.b
    Jun 16, 2017 at 15:11
  • $\begingroup$ @Remi.b they are? They work fine for me, that sounds like a bug. Anyway, glad I could help :) $\endgroup$
    – terdon ♦
    Jun 16, 2017 at 15:16
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Promoters and enhancers based on CAGE-seq from FANTOM5: http://fantom.gsc.riken.jp/5/data/

Just choose the category and download bed-file, e.g. CAGE-peaks would be promoters. There are READMEs in each folder that explain the data.

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