<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi DK,<div class=""><br class=""></div><div class="">you have a few options of getting allele frequencies for a variant.</div><div class=""><br class=""></div><div class="">You can use</div><div class=""> - our perl API: <a href="http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#alleles" class="">http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#alleles</a> (to get you started)</div><div class=""> - our REST API: <a href="https://rest.ensembl.org/documentation/info/variation_id" class="">https://rest.ensembl.org/documentation/info/variation_id</a> (to get you started)</div><div class=""> - the VEP: <a href="https://www.ensembl.org/info/docs/tools/vep/script/vep_options.html" class="">https://www.ensembl.org/info/docs/tools/vep/script/vep_options.html</a> It will allow you to annotate your input variants with frequency data if available</div><div class=""><br class=""></div><div class="">Please feel free to contact us again if you have any questions regarding the above approaches.</div><div class=""><br class=""></div><div class="">Kind regards,</div><div class="">Anja</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On 19 Sep 2017, at 16:06, deepak kumar <<a href="mailto:deepak.k.choubey@gmail.com" class="">deepak.k.choubey@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Dear ALL,<div class=""><br class=""></div><div class=""><span style="color:rgb(51,51,51);font-family:sans-serif;font-size:13px" class=""> I have been looking for a way to find "which nsSNP (with rs ID number like rs769971095) belong to what population(s), and if possible what gender"? I came to know about the Ensembl "population genetics" for the variants. </span><br class=""></div><div class=""><span style="color:rgb(51,51,51);font-family:sans-serif;font-size:13px" class=""><br class=""></span></div><div class=""><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(102,102,102);font-family:sans-serif;font-size:13px" class="">I found the respective population genetics info for 2 rsIDs; rs559632360 & rs769971095</p><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(102,102,102);font-family:sans-serif;font-size:13px" class="">For "rs769971095" the super-population it shows is: ALL, AFR, AMR, ASJ, EAS, FIN, NFE, OTH, SAS. </p><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(102,102,102);font-family:sans-serif;font-size:13px" class="">For "rs559632360" the super-population it shows is: ALL, AFR, AMR, EAS, SAS, EUR.</p><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(102,102,102);font-family:sans-serif;font-size:13px" class=""><br class=""></p><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(102,102,102);font-family:sans-serif;font-size:13px" class="">For rs559632360 rsID, it also shows population genetics from "1000 Genomes Project Phase 3 & gnomAD exomes" along with "subpopulation" information, whereas, for rs769971095 it shows only "gnomAD exomes" population genetics.</p><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(102,102,102);font-family:sans-serif;font-size:13px" class=""><a rel="nofollow" href="http://grch37.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=3:12625875-12626875;v=rs769971095;vdb=variation;vf=135759093" style="box-sizing:border-box;background:transparent;color:rgb(66,139,202);text-decoration-line:none" class="">http://grch37.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=3:12625875-12626875;v=rs769971095;vdb=variation;vf=135759093</a></p><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(102,102,102);font-family:sans-serif;font-size:13px" class=""><a rel="nofollow" href="http://grch37.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=3:12632759-12633759;v=rs559632360;vdb=variation;vf=92299087#population_freq_SAS" style="box-sizing:border-box;background:transparent;color:rgb(66,139,202);text-decoration-line:none" class="">http://grch37.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=3:12632759-12633759;v=rs559632360;vdb=variation;vf=92299087#population_freq_SAS</a></p><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(102,102,102);font-family:sans-serif;font-size:13px" class="">Does this mean that for "rs769971095" there is no "1000 genomes project phase 3" data available? </p><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(102,102,102);font-family:sans-serif;font-size:13px" class="">I am interested to know if these two rsIDs belong to one population, so, can it be said that these rsIDs share same population? If yes, what population they share? It would be great if I could know how to make a reasonable interpretation for this.</p><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(102,102,102);font-family:sans-serif;font-size:13px" class="">Also, I need to do this for many rsIDs, could you please let me know how this process can be automated? Where, I can generate results like this:</p><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(102,102,102);font-family:sans-serif;font-size:13px" class=""><br class=""></p><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(102,102,102);font-family:sans-serif;font-size:13px" class=""><b class="">rsID Super-Population with allele frequencies Sub-population</b></p><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(102,102,102);font-family:sans-serif;font-size:13px" class="">rs769971095 ALL, AFR, AMR, ASJ, EAS, FIN, NFE, OTH, SAS. .......etc</p><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(102,102,102);font-family:sans-serif;font-size:13px" class="">rs559632360 ALL, AFR, AMR, EAS, SAS, EUR ......etc </p><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(102,102,102);font-family:sans-serif;font-size:13px" class=""><br class=""></p><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(102,102,102);font-family:sans-serif;font-size:13px" class=""><br class=""></p><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(102,102,102);font-family:sans-serif;font-size:13px" class="">Thanks much! DK</p></div></div>
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