Database for finding SNPs (Mutation-deletion/SNPs) In the promotor region of any gene
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7.1 years ago
vrun.bnsl ▴ 10

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 gene genome sequence • 4.9k views
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7.1 years ago
David Fredman ★ 1.1k

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:

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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

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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/).

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7.1 years ago

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/

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