<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 DK,<div class=""><br class=""></div><div class="">for a) you can use our lookup endpoint</div><div class=""><a href="https://rest.ensembl.org/documentation/info/lookup" class="">https://rest.ensembl.org/documentation/info/lookup</a></div><div class=""><br class=""></div><div class="">for your example:</div><div class=""><a href="https://rest.ensembl.org/lookup/id/NM_007299.3?content-type=application/json;expand=1;utr=1" class="">https://rest.ensembl.org/lookup/id/NM_007299.3?content-type=application/json;expand=1;utr=1</a></div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">for b) you can use the ID overlap endpoint:</div><div class=""><a href="https://rest.ensembl.org/documentation/info/overlap_id" class="">https://rest.ensembl.org/documentation/info/overlap_id</a></div><div class=""><br class=""></div><div class="">In order to get all overlapping variants for a transcript you use the endpoint like this:</div><div class=""><a href="https://rest.ensembl.org/overlap/id/NM_007299.3?feature=variation;content-type=application/json" class="">https://rest.ensembl.org/overlap/id/NM_007299.3?feature=variation;content-type=application/json</a></div><div class=""><br class=""></div><div class="">To only return variants in 5’ and 3’ UTRs you can add additional filters to the request:</div><div class=""><a href="https://rest.ensembl.org/overlap/id/NM_007299.3?feature=variation&so_term=3_prime_UTR_variant;so_term=5_prime_UTR_variant;content-type=application/json" class="">https://rest.ensembl.org/overlap/id/NM_007299.3?feature=variation&so_term=3_prime_UTR_variant;so_term=5_prime_UTR_variant;content-type=application/json</a></div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">For each variant in our database we compute its consequence on overlapping transcripts. We use sequence ontology terms for describing the consequences. You can find a ranked list of all the SO terms we assign here: <a href="http://www.ensembl.org/info/genome/variation/predicted_data.html#consequences" class="">http://www.ensembl.org/info/genome/variation/predicted_data.html#consequences</a></div><div class=""><br class=""></div><div class=""><div class="">We do compute 5_prime_UTR_variant and 3_prime_UTR_variant consequences which allows you to filter for only those variants.</div><div class=""><br class=""></div><div class="">However, for each variant that we return in the overlap endpoint we only report the most severe consequence for the given variant and overlapping transcript. Sometimes the returned consequence_type will be different from 5_prime_UTR_variant and 3_prime_UTR_variant because the variant is not only a 5 prime UTR variant but also for example causes a frameshift. In this case the consequence type is frameshift variant.</div></div><div class=""><br class=""></div><div class="">If you want a detailed list of all the consequences for all variants in a 3’ and 5’ region you need to first retrieve all the variants from the overlap endpoint and then use the variants as input for the VEP endpoint.</div><div class=""><br class=""></div><div class="">Best,</div><div class="">Anja</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On 23 Sep 2017, at 14:17, 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="">Thanks much Anja! <div class=""><br class=""></div><div class="">I think Ensembl is a very useful platform for such queries. Am curious for this following query below, could you please let me know how can I do this using the Ensembl platform:</div><div class=""><br class=""></div><div class="">a) I want to extract the 5' and 3' UTRs from the mRNA of BRCA1 and BRCA2. For instance information 5' & 3' UTR for the refseq geneid "<span style="font-size: inherit; word-spacing: normal; font-family: Consolas, Monaco, 'Andale Mono', 'Ubuntu Mono', monospace;" class="">NM_007299.3</span>" of BRCA1</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">b) Also, find the position of the SNPs (rsIDs) in the 5' and 3' UTRs. For instance information like this: (for the refseq geneid "<span style="font-family: Consolas, Monaco, 'Andale Mono', 'Ubuntu Mono', monospace; font-size: inherit; word-spacing: normal;" class="">NM_007299.3</span>" of BRCA1)</div><div class=""> </div><div class="">refseg-geneID mutant-allele position-of-mutation</div><div class=""><span style="font-family: Consolas, Monaco, 'Andale Mono', 'Ubuntu Mono', monospace;" class="">NM_007299.3 c to t 400032</span><br class=""></div><div class=""><br class=""></div><div class="">Thanks much! Please let me know if something is not clear.</div><div class=""><br class=""></div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Thu, Sep 21, 2017 at 1:07 PM, Anja Thormann <span dir="ltr" class=""><<a href="mailto:anja@ebi.ac.uk" target="_blank" class="">anja@ebi.ac.uk</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" class="">Hi DK,<div class=""><br class=""></div><div class=""><div class="">Let me give you some background on where we get our data for allele frequency or genotype frequency annotations from:</div><div class=""><br class=""></div><div class="">We provide allele frequencies and genotype frequencies (where available) from a set of reference populations provided by projects like 1000 Genomes Project, ESP, gnomAD (supersedes ExAC).</div><div class=""><br class=""></div><div class="">Only 1000 Genomes provides sample genotypes from which we can compute population genotype frequencies.</div><div class=""><br class=""></div><div class="">ESP provides population genotype frequencies. But we don't get a break down of genotypes by sample in the population.</div><div class=""><br class=""></div><div class="">gnomAD only provides allele counts in a population.</div><div class=""><br class=""></div><div class="">Here is a variant which has annotations from all of the above projects: <a href="http://www.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=1:230709548-230710548;v=rs699;vdb=variation;vf=664" target="_blank" class="">http://www.ensembl.org/Homo_<wbr class="">sapiens/Variation/Population?<wbr class="">db=core;r=1:230709548-<wbr class="">230710548;v=rs699;vdb=<wbr class="">variation;vf=664</a></div><div class=""><br class=""></div><div class="">For 1000GENOMES:phase_3:AFR allele frequencies: A: 0.097 G: 0.903 genotype frequencies: A|A: 0.126 A|G: 0.338 G|G: 0.536</div><div class="">For gnomADe:AFR allele frequencies: A: 0.152 G: 0.848 No genotype frequencies</div><div class=""><br class=""></div><div class="">Our variation endpoint does not return gnomAD frequencies at the moment. We will include the frequencies for the next release.</div><div class=""><br class=""></div><div class="">For now I would recommend that you use our VEP endpoint</div><div class=""><a href="https://rest.ensembl.org/documentation/info/vep_id_get" target="_blank" class="">https://rest.ensembl.org/<wbr class="">documentation/info/vep_id_get</a></div><div class="">Examples:</div><div class=""><a href="https://rest.ensembl.org/vep/human/id/rs769971095?content-type=application/json" target="_blank" class="">https://rest.ensembl.org/vep/<wbr class="">human/id/rs769971095?content-<wbr class="">type=application/json</a></div><div class=""><a href="https://rest.ensembl.org/vep/human/id/rs699?content-type=application/json" target="_blank" class="">https://rest.ensembl.org/vep/<wbr class="">human/id/rs699?content-type=<wbr class="">application/json</a></div><div class=""><br class=""></div><div class="">The VEP makes use of cache files which store allele frequencies for the 1000 Genomes Project super populations (AFR, AMR, EAS, EUR, SAS) and the gnomAD exome data.</div><div class=""><br class=""></div><div class="">Please find a list of our populations, their short names and descriptions here:</div><div class=""><a href="http://www.ensembl.org/info/genome/variation/data_description.html#populations" target="_blank" class="">http://www.ensembl.org/info/<wbr class="">genome/variation/data_<wbr class="">description.html#populations</a></div><div class=""><br class=""></div><div class="">The VEP provides annotations from:</div><div class="">gnomADe:ALL - All gnomAD exomes individuals</div><div class="">gnomADe:AFR - African/African American</div><div class="">gnomADe:AMR - Admixed American</div><div class="">gnomADe:ASJ - Ashkenazi Jewish</div><div class="">gnomADe:EAS - East Asian</div><div class="">gnomADe:FIN - Finnish</div><div class="">gnomADe:NFE - Non-Finnish European</div><div class="">gnomADe:OTH - Other</div><div class="">gnomADe:SAS - South Asian</div><div class="">1000GENOMES:phase_3:AFR African</div><div class="">1000GENOMES:phase_3:AMR American</div><div class="">1000GENOMES:phase_3:EAS East Asian</div><div class="">1000GENOMES:phase_3:EUR European</div><div class="">1000GENOMES:phase_3:SAS South Asian</div><div class=""><br class=""></div><div class="">The populations use the following names in the vep endpoints:</div><div class=""> - for example for gnomADe:NFE: gnomad_nfe_maf and gnomad_nfe_allele</div><div class=""> - for example for 1000GENOMES:phase_3:AFR: afr_maf and afr_allele</div><div class=""><br class=""></div><div class="">We have a post vep endpoint which allows you to send a list of variant IDs for annotation. <a href="https://rest.ensembl.org/documentation/info/vep_id_post" target="_blank" class="">https://rest.<wbr class="">ensembl.org/documentation/<wbr class="">info/vep_id_post</a></div><div class=""><br class=""></div><div class=""><div class="">I hope that helps you with your use case.</div><span class="HOEnZb"><font color="#888888" class=""><div class=""><br class=""></div><div class="">Anja</div></font></span></div><div class=""><div class="h5"><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><blockquote type="cite" class=""><div class="">On 20 Sep 2017, at 22:05, deepak kumar <<a href="mailto:deepak.k.choubey@gmail.com" target="_blank" class="">deepak.k.choubey@gmail.com</a>> wrote:</div><br class="m_-1526393040704610493Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi Anja,<div class=""><br class=""></div><div class="">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 class=""><br class=""></div><div class="">To start of with, I find the "Rest API" a very clean approach to get variant information.</div><div class=""><br class=""></div><div class="">a) My aim is to find if a SNP (rsID let say <span style="font-family:Times;font-size:inherit" class="">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 class=""><br class=""></div><div class="">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 class=""><br class=""></div><div class="">Thanks much!</div><div class="">DK</div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Tue, Sep 19, 2017 at 7:22 PM, Anja Thormann <span dir="ltr" class=""><<a href="mailto:anja@ebi.ac.uk" target="_blank" class="">anja@ebi.ac.uk</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" 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" target="_blank" class="">http://www.ensembl.org/in<wbr class="">fo/docs/api/variation/variatio<wbr class="">n_tutorial.html#alleles</a> (to get you started)</div><div class=""> - our REST API: <a href="https://rest.ensembl.org/documentation/info/variation_id" target="_blank" class="">https://rest.ensembl.org/<wbr class="">documentation/info/variation_i<wbr class="">d</a> (to get you started)</div><div class=""> - the VEP: <a href="https://www.ensembl.org/info/docs/tools/vep/script/vep_options.html" target="_blank" class="">https://www.ensembl.org/i<wbr class="">nfo/docs/tools/vep/script/vep_<wbr class="">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 class=""><blockquote type="cite" class=""><div class=""><div class="m_-1526393040704610493h5"><div class="">On 19 Sep 2017, at 16:06, deepak kumar <<a href="mailto:deepak.k.choubey@gmail.com" target="_blank" class="">deepak.k.choubey@gmail.com</a>> wrote:</div><br class="m_-1526393040704610493m_5289383583780598652Apple-interchange-newline"></div></div><div class=""><div class=""><div class="m_-1526393040704610493h5"><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" target="_blank" class="">http://grch37.ensembl.org/Homo<wbr class="">_sapiens/Variation/Population?<wbr class="">db=core;r=3:12625875-12626875;<wbr class="">v=rs769971095;vdb=variation;<wbr class="">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" target="_blank" class="">http://grch37.ensembl.org/Homo<wbr class="">_sapiens/Variation/Population?<wbr class="">db=core;r=3:12632759-12633759;<wbr class="">v=rs559632360;vdb=variation;<wbr class="">vf=92299087#population_freq_<wbr class="">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></div></div>
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