[BioMart Users] dbSNPs with functional category

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[BioMart Users] dbSNPs with functional category

Tesfaye Mersha
Hi
 
I am looking SNP database which link SNPs with its functional classification like synonymous SNP, nonsynonymous SNP and other types.
 
I wish if you send me any Ensembl help resources as well as databases.
Thanks,
Tes
 
Tesfaye B. Mersha, Ph.D.
Assistant Professor
Cincinnati Children's Hospital Medical Center
Department of Pediatrics
University of Cincinnati
phone 513-803-2766
[hidden email]

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Re: [BioMart Users] dbSNPs with functional category

Elena Rivkin
Hi Tesfaye, 

In BioMart Martview (www.biomart.org/biomart/martview) you can query Ensembl variation data by selecting the following:

Database: Ensembl variaiton 63 
Dataset relevant to your species of interest (e.g. Homo sapiens Variation (dbSNP 132;ENSEMBL)

When you do that, you will see a selection of Filters and Attributes.  For example, under the GENE ASSOCIATED VARIATION FILTERS, you can select the Consequence type to include only synonymous SNPs, non-synonymous SNPS, and others (you can select multiple with the ctrl key)

Finally, select Attributes (eg. SNP ID, location, Ensembl Gene id, etc). 
Click on Results to view the data. 

Please let me know if you have other questions. 
 

Elena Rivkin, PhD
Outreach and Training Coordinator, Informatics and Bio-computing

Ontario Institute for Cancer Research
MaRS Centre, South Tower

101 College Street, Suite 800

Toronto, Ontario, Canada M5G 0A3


Tel: 647-258-4316

Toll-free: 1-866-678-6427

www.oicr.on.ca


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From: Tesfaye Mersha <[hidden email]>
Date: Thu, 1 Sep 2011 10:07:42 -0400
To: "[hidden email]" <[hidden email]>
Subject: [BioMart Users] dbSNPs with functional category

Hi
 
I am looking SNP database which link SNPs with its functional classification like synonymous SNP, nonsynonymous SNP and other types.
 
I wish if you send me any Ensembl help resources as well as databases.
Thanks,
Tes
 
Tesfaye B. Mersha, Ph.D.
Assistant Professor
Cincinnati Children's Hospital Medical Center
Department of Pediatrics
University of Cincinnati
phone 513-803-2766
[hidden email]

_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users