Closest (Distance, Bp) Promotor To A Snp

Question

[Sander Timmer]

Before I start writing some basic Perl scrips I was wondering if I could use any of the genome browsers or biomart to just upload a list with locations or SNP identifiers to find out for each of these SNPs what the closest gene and what the closest promotor is. Closest in this case means bp distance.

Is there any out of the box solution that I can use in Humans (in the hg19 genome build) or should I just code something simple in the Ensembl API to get this task done? Question seems fairly simple and is (I think) fairly common so I'd expect that there are out-of-the-box solutions though with Google I don't seem to find anything that looks like what I want!

Anyone with an early christmas present for me?! :-)

Answer 1

[Wolf]

bedtools (http://code.google.com/p/bedtools/) closestBed will do what you need

[Sander Timmer]

Great, this seem to be what I was looking for, not sure why I couldn't find it myself.

Answer 2

[Sean Davis]

Galaxy has a tool for genomic interval manipulation and for finding the closest genomic interval (either stranded or not). You can get data from UCSC or Ensembl and then use "Operate on Genomic Intervals" tools to answer your question.

[Sander Timmer]

Could have selected your answer as the "best" as well! Thanks for the input but I already got it working with bedtools

Answer 3

[Larry_Parnell]

I think it might be more productive to search the questions here at BioStar, and perhaps at other such sites, as this question has appeared earlier.

This is certainly so if you just want to map the SNPs to the nearest genome annotation, eg, gene or promoter region. Then, one could ask, well, what do you want to do with these SNPs? That is an important question as it informs how to go about collecting the information you wish to have, and perhaps which other info is also vital to your downstream efforts.

[Sander Timmer]

Its just for getting a brief overview of a couple of 100 SNPs identified in a test on their relative location in respect to some genomic entities. I've searched biostar before but what I found was more related to people that wanted to do things like seeing if its inside a promotor or to get the translational effect of the SNP not really to get relative distance to a genomic entity.

I think I'll stick with the bedtools solution from the other answer.

Answer 4

[Yuyin110]

First you can use the UCSC find the gene and mRNA accession with your SNPs location, then following the mRNA accession, you can find the promoter region you want at DBTSS.