<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:dt="uuid:C2F41010-65B3-11d1-A29F-00AA00C14882" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:Helvetica;
panose-1:2 11 6 4 2 2 2 2 2 4;}
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:#0563C1;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:#954F72;
text-decoration:underline;}
pre
{mso-style-priority:99;
mso-style-link:"HTML Preformatted Char";
margin:0in;
margin-bottom:.0001pt;
font-size:10.0pt;
font-family:"Courier New";}
span.EmailStyle17
{mso-style-type:personal-compose;
font-family:"Calibri",sans-serif;
color:windowtext;}
span.HTMLPreformattedChar
{mso-style-name:"HTML Preformatted Char";
mso-style-priority:99;
mso-style-link:"HTML Preformatted";
font-family:"Courier New";}
.MsoChpDefault
{mso-style-type:export-only;
font-family:"Calibri",sans-serif;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang="EN-US" link="#0563C1" vlink="#954F72">
<div class="WordSection1">
<p class="MsoNormal">How can I programmatically retrieve variants that are associated with a phenotype and ASSOCIATED with a gene, even if the variant is not strictly within a gene’s boundaries?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">If you visit <a href="http://useast.ensembl.org/Homo_sapiens/Gene/Phenotype?db=core;g=ENSG00000073756;r=1:186671791-186680427#ALL_tablePanel">
http://useast.ensembl.org/Homo_sapiens/Gene/Phenotype?db=core;g=ENSG00000073756;r=1:186671791-186680427#ALL_tablePanel</a>, under “ALL associated variants” you will see
<a href="http://useast.ensembl.org/Homo_sapiens/Variation/Phenotype?db=core;g=ENSG00000073756;r=1:186671791-186680427;v=rs10489403">
<span style="font-size:9.5pt;font-family:"Helvetica",sans-serif;color:#000066;background:white">rs10489403</span></a> associated with hematocrit phenotypes.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">If I query biomart for variants and phenotypes associated with ENSG00000073756,
<a href="http://useast.ensembl.org/Homo_sapiens/Variation/Phenotype?db=core;g=ENSG00000073756;r=1:186671791-186680427;v=rs10489403">
<span style="font-size:9.5pt;font-family:"Helvetica",sans-serif;color:#000066;background:white">rs10489403</span></a> is not listed.
<o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:black"> <Dataset name = "hsapiens_snp" interface = "default" ><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:black"> <Filter name = "ensembl_gene" value = "ENSG00000073756"/><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:black"> <Attribute name = "refsnp_id" /><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:black"> <Attribute name = "ensembl_gene_stable_id" /><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:black"> <Attribute name = "associated_gene" /><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:black"> </Dataset><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:black"><o:p> </o:p></span></p>
<p class="MsoNormal">If I look for <a href="http://useast.ensembl.org/Homo_sapiens/Variation/Phenotype?db=core;g=ENSG00000073756;r=1:186671791-186680427;v=rs10489403">
<span style="font-size:9.5pt;font-family:"Helvetica",sans-serif;color:#000066;background:white">rs10489403</span></a> in the web interface or biomart, I see that it is intergenic between PGTS2 and PLA2G4A.<o:p></o:p></p>
<pre><span style="color:black"> <Dataset name = "hsapiens_snp" interface = "default" ><o:p></o:p></span></pre>
<pre><span style="color:black"> <Filter name = "snp_filter" value = "rs10489403"/><o:p></o:p></span></pre>
<pre><span style="color:black"> <Attribute name = "refsnp_id" /><o:p></o:p></span></pre>
<pre><span style="color:black"> <Attribute name = "ensembl_gene_stable_id" /><o:p></o:p></span></pre>
<pre><span style="color:black"> <Attribute name = "associated_gene" /><o:p></o:p></span></pre>
<pre><span style="color:black"> </Dataset><o:p></o:p></span></pre>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">It doesn’t seem like <span style="color:black">associated_gene</span> is a filterable field. How can I query biomart, or MySQL directly, with ENSG00000073756 as my gene of interest and retrieve
<a href="http://useast.ensembl.org/Homo_sapiens/Variation/Phenotype?db=core;g=ENSG00000073756;r=1:186671791-186680427;v=rs10489403">
<span style="font-size:9.5pt;font-family:"Helvetica",sans-serif;color:#000066;background:white">rs10489403</span></a> as a variant which has PTGS2/ ENSG00000073756 as an associated gene?<o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Thanks,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Mark</span><b><i><o:p></o:p></i></b></p>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<p class="MsoNormal" style="text-align:justify"><span style="font-size:8.0pt;font-family:Arial">The contents of this e-mail message, including any attachments, are intended solely for the use of the person or entity to which the e-mail was addressed. If you
are not the intended recipient of this message, be advised that any dissemination, distribution, or use of the contents of this message is strictly prohibited. If you received this e-mail message in error, please e-mail
<a href=" is@instem.com" ?="">is@instem.com</a> and contact the sender by reply e-mail. Please also permanently delete all copies of the original e-mail and any attached documentation. Thank you. Copyright 2016 Instem Group of Companies. For any other correspondence
please write to Instem plc. a company registered in England and Wales, number 07148099, with registered office at Diamond Way, Stone Business Park, Stone, Staffordshire, ST15 0SD England.</span></p>
</body>
</html>