<div dir="ltr"><div><div><div><div><div>Hi Joe,<br><br></div>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 <a href="http://ensembl.gramene.org/Oryza_sativa/Variation/Summary?db=core;r=1:27974409-27974429;source=dbSNP;v=rs21489235;vdb=variation;vf=1004333">http://ensembl.gramene.org/Oryza_sativa/Variation/Summary?db=core;r=1:27974409-27974429;source=dbSNP;v=rs21489235;vdb=variation;vf=1004333</a> but other SNPs like the second in your list do not seem to exist in our database.<br>
<br></div><div>For bulk downloads for various genomic regions, the Gramene Mart utility at <a href="http://ensembl.gramene.org/biomart/martview">http://ensembl.gramene.org/biomart/martview</a> might be most useful. Make sure to select "Plant Variation" database.<br>
</div><div><br></div>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 <a href="ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/data/qtl/">ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/data/qtl/</a><br>
</div>You could attempt doing so yourself with our Assembly Converter Tool at <a href="http://ensembl.gramene.org/tools.html">http://ensembl.gramene.org/tools.html</a> but be warned that mapping is not straight forward for inprecise regions such as QTLs.<br>
<br></div>Hope this helps,<br></div><br>Marcela<br><div><div><br><div><div><br></div></div></div></div></div><div class="gmail_extra"><br clear="all"><div><span style="border-collapse:collapse;color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px"><font size="1">==<br>
Marcela Karey Monaco, PhD</font> <font size="1"><br>Gramene Project Coordinator<br>Cold Spring Harbor Laboratory<br>One Bungtown Road, Williams #5<br>Cold Spring Harbor, NY 11724<br></font></span><span style="border-collapse:collapse;color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px"><font size="1">Phone: <a value="+15163676998" style="color:rgb(17,85,204)"><span>516</span>-<span>367</span>-<span><span style="background-image:initial;background-color:rgb(255,255,204);color:rgb(34,34,34);background-repeat:initial initial"><span><font size="1">8808</font></span></span></span></a><a value="+15163676998" style="color:rgb(17,85,204)"><span></span></a><br>
Fax: <a value="+15163676851" style="color:rgb(17,85,204)"><span>516</span>-<span>367</span>-6851</a></font></span></div>
<br><br><div class="gmail_quote">On Tue, Apr 8, 2014 at 4:00 PM, <a href="mailto:feedback@gramene.org">feedback@gramene.org</a> <span dir="ltr"><<a href="mailto:feedback@gramene.org" target="_blank">feedback@gramene.org</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">URL : <a href="http://www.gramene.org/" target="_blank">http://www.gramene.org/</a><br>
<br>
Subject : Site Feedback: SNP locations<br>
<br>
Name : Joe Kepiro<br>
<br>
Email : <a href="mailto:jkepiro@riceresearchers.com">jkepiro@riceresearchers.com</a><br>
<br>
Organization: rice researchers inc.<br>
<br>
Comments :<br>
<br>
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<br>
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SNP CHR POS<br>
OsSNP0230 1 27974409<br>
OsSNP0258 1 31337713<br>
OsSNP0277 1 33605643<br>
OsSNP0351 1 42590276<br>
OsSNP0358 1 43447475<br>
OsSNP2101 8 9478728<br>
OsSNP2730 11 11885702<br>
OsSNP2763 11 15858218<br>
OsSNP2916 12 12100929<br>
<br>
<br>
<a href="http://www.warelab.org/bugs/view.php?id=4921" target="_blank">http://www.warelab.org/bugs/view.php?id=4921</a><br>
<br>
<br>
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