<div dir="ltr">Hi Anja,<div><br></div><div>Thank you so much for the reply. It certainly helped me to get to the right direction of my query. However, could you please help me understand a few queries regarding the same:</div><div><br></div><div>To start of with, I find the "Rest API" a very clean approach to get variant information.</div><div><br></div><div>a) My aim is to find if a SNP (rsID let say <span style="color:rgb(0,0,0);font-family:Times;font-size:medium">rs769971095</span>) share populations, or in other words, if this rsID mutation can be found in more than one population. From the links you provided I see that I can find an answer but am confused between "population allele frequency" and "population genotype frequency". To fulfill my aim, data for this rsID should be taken from "population allele frequency" or "population genotype frequency"?</div><div><br></div><div>b) The population name given in the "example output" of the "Rest API" are in short form like 'AMR', 'SAS' etc. Could you please let me know how can i retrieve the full population name for a given rsID?</div><div><br></div><div>Thanks much!</div><div>DK</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Sep 19, 2017 at 7:22 PM, Anja Thormann <span dir="ltr"><<a href="mailto:anja@ebi.ac.uk" target="_blank">anja@ebi.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hi DK,<div><br></div><div>you have a few options of getting allele frequencies for a variant.</div><div><br></div><div>You can use</div><div> - our perl API: <a href="http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#alleles" target="_blank">http://www.ensembl.org/<wbr>info/docs/api/variation/<wbr>variation_tutorial.html#<wbr>alleles</a> (to get you started)</div><div> - our REST API: <a href="https://rest.ensembl.org/documentation/info/variation_id" target="_blank">https://rest.ensembl.org/<wbr>documentation/info/variation_<wbr>id</a> (to get you started)</div><div> - the VEP: <a href="https://www.ensembl.org/info/docs/tools/vep/script/vep_options.html" target="_blank">https://www.ensembl.org/<wbr>info/docs/tools/vep/script/<wbr>vep_options.html</a> It will allow you to annotate your input variants with frequency data if available</div><div><br></div><div>Please feel free to contact us again if you have any questions regarding the above approaches.</div><div><br></div><div>Kind regards,</div><div>Anja</div><div><br></div><div><br><div><blockquote type="cite"><div><div class="h5"><div>On 19 Sep 2017, at 16:06, deepak kumar <<a href="mailto:deepak.k.choubey@gmail.com" target="_blank">deepak.k.choubey@gmail.com</a>> wrote:</div><br class="m_5289383583780598652Apple-interchange-newline"></div></div><div><div><div class="h5"><div dir="ltr">Dear ALL,<div><br></div><div><span style="color:rgb(51,51,51);font-family:sans-serif;font-size:13px"> 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></div><div><span style="color:rgb(51,51,51);font-family:sans-serif;font-size:13px"><br></span></div><div><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(102,102,102);font-family:sans-serif;font-size:13px">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">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">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"><br></p><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(102,102,102);font-family:sans-serif;font-size:13px">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"><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" target="_blank">http://grch37.ensembl.org/<wbr>Homo_sapiens/Variation/<wbr>Population?db=core;r=3:<wbr>12625875-12626875;v=<wbr>rs769971095;vdb=variation;vf=<wbr>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"><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" target="_blank">http://grch37.ensembl.org/<wbr>Homo_sapiens/Variation/<wbr>Population?db=core;r=3:<wbr>12632759-12633759;v=<wbr>rs559632360;vdb=variation;vf=<wbr>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">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">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">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"><br></p><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(102,102,102);font-family:sans-serif;font-size:13px"><b>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">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">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"><br></p><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(102,102,102);font-family:sans-serif;font-size:13px"><br></p><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(102,102,102);font-family:sans-serif;font-size:13px">Thanks much! DK</p></div></div></div></div>
______________________________<wbr>_________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/<wbr>mailman/listinfo/dev</a><br>Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br></div></blockquote></div><br></div></div><br>______________________________<wbr>_________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" rel="noreferrer" target="_blank">http://lists.ensembl.org/<wbr>mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" rel="noreferrer" target="_blank">http://www.ensembl.info/</a><br>
<br></blockquote></div><br></div>