[ensembl-dev] [1000G #353572] How to get population names for SNP from homo_sapiens_variation_73_37 - browser.1000genomes.org

[Patricia Buendia]

To the dev mailing list:

I would very much appreciate getting some help with this question:

I have a question regarding the Ensembl mySQL database. I do not want to use the API but directly query the database.

What SQL statement would I use to obtain the records shown in http://browser.1000genomes.org/Homo_sapiens/Variation/Population?db=core;g=ENSG00000134242;r=1:114356433-114414381;source=dbSNP;v=rs114092230;vdb=variation;vf=27418953#_

for SNP rs114092230?

When running an SQL query linking the population, allele and variation tables in homo_sapiens_variation_73_37, I get only population.name= "1000GENOMES:pilot_1_YRI_low_coverage_panel" for that SNP, but the above link shows many more populations. How do I get the same data using an SQL statement.

Paty


-----Original Message-----
From: Laura Clarke via RT [mailto:info at 1000genomes.org]
Sent: Friday, September 13, 2013 2:33 PM
To: paty at infotechsoft.com
Subject: [1000G #353572] How to get population names for SNP from homo_sapiens_variation_73_37 - browser.1000genomes.org

I would recommend reading the tutorial

http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html

and if that doesn't help email the dev mailing list

thanks

Laura

On Fri Sep 13 18:35:28 2013, paty at infotechsoft.com wrote:
> Thank you, Laura. So I just have to wait and don't need to send an 
> email to dev at ensembl.org?
> Paty
>
> -----Original Message-----
> From: Laura Clarke via RT [mailto:info at 1000genomes.org]
> Sent: Friday, September 13, 2013 4:19 AM
> To: paty at infotechsoft.com
> Subject: [1000G #353572] How to get population names for SNP from
> homo_sapiens_variation_73_37 - browser.1000genomes.org
>
> Fri Sep 13 09:19:18 2013: Request 353572 was acted upon.
> Transaction: Taken by laura at ebi.ac.uk
> Queue: 1000genomes
> Subject: How to get population names for SNP from
> homo_sapiens_variation_73_37 - browser.1000genomes.org
> Owner: laura at ebi.ac.uk
> Requestors: paty at infotechsoft.com
> Status: new
> Ticket <URL: https://rt.sanger.ac.uk/Ticket/Display.html?id=353572 >
>
>
> Your ticket has been assigned to an engineer, as shown in the Owner 
> field above.
>
> Regards,
> 1000 Genomes Project Helpdesk
> info at 1000genomes.org
>
>
>



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