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Hi Guys,</div>
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<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>
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<i>wget -q --header='Content-type:application/json' --header='Accept:application/json' --post-data='{ "ids" : ["rs1314913" ] }' 'http://grch37.rest.ensembl.org/variation/homo_sapiens?phenotypes=1' -O -</i></div>
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<div>The output looks alright, the variant has the expected phenotype annotation. But when querying the same region, the variant is not listed:</div>
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<i>wget -q 'http://grch37.rest.ensembl.org/overlap/region/human/14:68699592-68699596?feature=variation;content-type=application/json;variant_set=ph_variants' -O -</i></div>
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If the variant_set option is removed, the variant is there:</div>
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<i>wget -q 'http://grch37.rest.ensembl.org/overlap/region/human/14:68699592-68699596?feature=variation;content-type=application/json' -O -</i></div>
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This example works well on the newer genome build, so this issue is probably GRCh37 specific.</div>
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Thanks for your help!</div>
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Best,</div>
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Daniel</div>
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