[Feedback] Site Feedback: SNP locations

[Marcela K. Monaco]

Hi Joe,

I suggest that you download all the variants for which we have data in
Gramene in the regions that you are interested in, for example your first
SNP might be the same as rs21489235 in Chr1:27974410, see
http://ensembl.gramene.org/Oryza_sativa/Variation/Summary?db=core;r=1:27974409-27974429;source=dbSNP;v=rs21489235;vdb=variation;vf=1004333but
other SNPs like the second in your list do not seem to exist in our
database.

For bulk downloads for various genomic regions, the Gramene Mart utility at
http://ensembl.gramene.org/biomart/martview might be most useful.  Make
sure to select "Plant Variation" database.

As for proximity to QTLs, it might be a little trickier because our rice
QTLs have not yet been remapped to the current IRGSP1 assembly, see
ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/data/qtl/
You could attempt doing so yourself with our Assembly Converter Tool at
http://ensembl.gramene.org/tools.html but be warned that mapping is not
straight forward for inprecise regions such as QTLs.

Hope this helps,

Marcela



==
Marcela Karey Monaco, PhD
Gramene Project Coordinator
Cold Spring Harbor Laboratory
One Bungtown Road, Williams #5
Cold Spring Harbor, NY 11724
Phone: 516-367-8808
Fax: 516-367-6851


On Tue, Apr 8, 2014 at 4:00 PM, feedback at gramene.org
<feedback at gramene.org>wrote:

> URL         : http://www.gramene.org/
>
> Subject     : Site Feedback: SNP locations
>
> Name        : Joe Kepiro
>
> Email       : jkepiro at riceresearchers.com
>
> Organization: rice researchers inc.
>
> Comments    :
>
> I had DNA Landmarks run some random SNP to confirm heterozygosity in F1's.
>  How can I find there location and proximity to traits.  I have an excel
> sheet with the SNP information.  name-chrom-position
>
> SNP     CHR     POS
> OsSNP0230       1       27974409
> OsSNP0258       1       31337713
> OsSNP0277       1       33605643
> OsSNP0351       1       42590276
> OsSNP0358       1       43447475
> OsSNP2101       8       9478728
> OsSNP2730       11      11885702
> OsSNP2763       11      15858218
> OsSNP2916       12      12100929
>
>
> http://www.warelab.org/bugs/view.php?id=4921
>
>
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>
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