Question: Database for finding SNPs (Mutation-deletion/SNPs) In the promotor region of any gene
1
gravatar for vrun.bnsl
5.3 years ago by
vrun.bnsl10
Korea, Republic Of
vrun.bnsl10 wrote:

Is there any online database in which I can find the mutations in the promotor region of oncogenes. Cosmic and other databases are not good for that purpose.Any one ???

snp sequence genome gene • 4.5k views
ADD COMMENTlink modified 5.3 years ago by Charles Warden7.4k • written 5.3 years ago by vrun.bnsl10
2
gravatar for David Fredman
5.3 years ago by
David Fredman990
University of Bergen, Norway
David Fredman990 wrote:

There are many good alternatives. You could use

If you are also interested in SNPs with potential regulatory effect that are outside of the promoter, you can explore:

ADD COMMENTlink modified 5.3 years ago • written 5.3 years ago by David Fredman990

Thanks for your response but how to confine the result to promotor region only.Within 1000 bp. Sorry , I am new to bioinformatics. Still not get it.The snpEff tool i guess is only restricited to c.elegans not homo sapiens

ADD REPLYlink written 5.3 years ago by vrun.bnsl10

snpEff can be used with human data, to be sure.

However, if you wish you extract public SNPs that are found within given (custom chosen by you) genomic regions (e.g. within 1000 bp upstream of the transcription start sites of your genes of interest), I suggest you work through tutorials/peruse the documentation and then attempt to use either Biomart (linked to above), UCSC table browser (http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html), or Galaxy (https://usegalaxy.org/).

ADD REPLYlink written 5.3 years ago by David Fredman990
0
gravatar for Charles Warden
5.3 years ago by
Charles Warden7.4k
Duarte, CA
Charles Warden7.4k wrote:

ANNOVAR annotates disruptions of conserved transcription factor binding sites

http://www.openbioinformatics.org/annovar/

FunSeq gives scores for non-coding variants, but I personally prefer the ANNOVAR report.

http://funseq.gersteinlab.org/

ADD COMMENTlink written 5.3 years ago by Charles Warden7.4k
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