<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi,<div class=""><br class=""></div><div class="">Please forgive some naive REST eQTL questions.</div><div class=""><br class=""></div><div class="">The documentation says:</div><div class=""><br class=""></div><div class=""><table class="table table-striped" style="max-width: 100%; background-color: rgb(255, 255, 255); border-collapse: collapse; border-spacing: 0px; width: 1170px; margin-bottom: 20px; color: rgb(51, 51, 51); font-family: 'Helvetica Neue', Helvetica, Arial, sans-serif; font-size: 14px; orphans: 2; widows: 2;"><tbody class=""><tr class=""><td style="padding: 8px; line-height: 20px; vertical-align: top; border-top-width: 1px; border-top-style: solid; border-top-color: rgb(221, 221, 221); background-color: rgb(249, 249, 249);" class=""><a href="http://rest.ensembl.org/documentation/info/species_id" style="color: rgb(0, 136, 204); text-decoration: none;" class="">GET eqtl/stable_id/:species/:stable_id</a></td><td style="padding: 8px; line-height: 20px; vertical-align: top; border-top-width: 1px; border-top-style: solid; border-top-color: rgb(221, 221, 221); background-color: rgb(249, 249, 249);" class="">Returns the p-value for each SNP in a given gene (e.g. ENSG00000227232)</td></tr></tbody></table><div class="">1)</div><div class="">How is “in a given gene” defined?</div></div><div class=""><br class=""></div><div class="">If I query REST for the homo sapiens gene in the example/documentation (ENSG00000227232) without any tissue or variant-name restrictions, then 159,122 of the returned results have a “display_consequence” of “intergenic_variant”, which is unexpected relative to “in a given gene”.</div><div class=""><br class=""></div><div class="">The counts for each different display_consequence are shown below:</div><div class=""><br class=""></div><div class=""><div class=""><font face="Courier" class=""> 6366 'display_consequence' => '3_prime_UTR_variant'</font></div><div class=""><font face="Courier" class=""> 1070 'display_consequence' => '5_prime_UTR_variant'</font></div><div class=""><font face="Courier" class=""> 21006 'display_consequence' => 'downstream_gene_variant'</font></div><div class=""><font face="Courier" class=""> 2 'display_consequence' => 'inframe_deletion'</font></div><div class=""><font face="Courier" class=""> 159122 'display_consequence' => 'intergenic_variant'</font></div><div class=""><font face="Courier" class=""> 186614 'display_consequence' => 'intron_variant'</font></div><div class=""><font face="Courier" class=""> 1078 'display_consequence' => 'missense_variant'</font></div><div class=""><font face="Courier" class=""> 6794 'display_consequence' => 'non_coding_transcript_exon_variant'</font></div><div class=""><font face="Courier" class=""> 86 'display_consequence' => 'non_coding_transcript_variant'</font></div><div class=""><font face="Courier" class=""> 634 'display_consequence' => 'splice_region_variant'</font></div><div class=""><font face="Courier" class=""> 948 'display_consequence' => 'synonymous_variant'</font></div><div class=""><font face="Courier" class=""> 21868 'display_consequence' => 'upstream_gene_variant'</font></div></div><div class=""><br class=""></div><div class="">2)</div><div class="">Whereas the documentation says that the stable gene id applies to the location of the eQTL SNP, and no gene information is returned in the result, am I to assume that the stable gene used for the query is also the gene in which the expression-level differences were observed (i.e. no trans effects can be recovered)? Will the result for the same SNP vary according to the query gene? That is, if a particular SNP is in the intergenic region between two oppositely oriented genes, it seems possible for that SNP to have a cis effect on both those genes. To find such an occurrence, I would have to query by each gene separately?</div><div class=""><br class=""></div><div class="">Thanks for any guidance.</div><div class=""><br class=""></div><div class="">Best regards,</div><div class=""><br class=""></div><div class="">Andrew</div><div class=""><br class=""></div></body></html>