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<p>Hi Daniel,</p>
<p>Thanks for reporting this one. There is a data problem in the
GRCh37 database and GWAS catalog variants are not associated with
the 'NHGRI-EBI GWAS catalog' or 'ph_variants' set. Until we can
fix the data in our March release, this would have to be a two
step process, extracting all variants by region then looking up by
id to filter the for those with phenotype information.<br>
</p>
Best wishes,<br>
<br>
Sarah<br>
<br>
<div class="moz-cite-prefix">On 24/01/2017 12:39, Daniel Suveges
wrote:<br>
</div>
<blockquote cite="mid:D4ACFB86.3DB1A%25ds26@sanger.ac.uk"
type="cite">
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<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
Hi Guys,</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
<br>
</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
<br>
</div>
<div><font face="Calibri,sans-serif">I'm planning to use the
overlap endpoint of the REST API to get a list of variants
which have phenotype annotations using the '</font><font
face="Calibri,sans-serif">variant_set=</font><span
style="font-family: Calibri, sans-serif;">ph_variants' option.
However it does not work as I expected. </span><span
style="font-family: Calibri, sans-serif; font-size: 14px;">Let's
take a GWAS hit rs1314913, a variant with phenotype
annotation:</span></div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
<i><br>
</i></div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
<i>wget -q --header='Content-type:application/json'
--header='Accept:application/json' --post-data='{ "ids" :
["rs1314913" ] }'
'<a class="moz-txt-link-freetext" href="http://grch37.rest.ensembl.org/variation/homo_sapiens?phenotypes=1">http://grch37.rest.ensembl.org/variation/homo_sapiens?phenotypes=1</a>'
-O -</i></div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
<div><br>
</div>
<div>The output looks alright, the variant has the expected
phenotype annotation. But when querying the same region, the
variant is not listed:</div>
</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
<i><br>
</i></div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
<i>wget -q
'<a class="moz-txt-link-freetext" href="http://grch37.rest.ensembl.org/overlap/region/human/14:68699592-68699596?feature=variation;content-type=application/json;variant_set=ph_variants">http://grch37.rest.ensembl.org/overlap/region/human/14:68699592-68699596?feature=variation;content-type=application/json;variant_set=ph_variants</a>'
-O -</i></div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
<i><br>
</i></div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
If the variant_set option is removed, the variant is there:</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
<br>
</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
<i>wget -q
'<a class="moz-txt-link-freetext" href="http://grch37.rest.ensembl.org/overlap/region/human/14:68699592-68699596?feature=variation;content-type=application/json">http://grch37.rest.ensembl.org/overlap/region/human/14:68699592-68699596?feature=variation;content-type=application/json</a>'
-O -</i></div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
<i><br>
</i></div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
This example works well on the newer genome build, so this issue
is probably GRCh37 specific.</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
Thanks for your help!</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
<br>
</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
Best,</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
Daniel</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
<br>
</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
<br>
</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
<br>
</div>
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