Answers.Body: <p>If your dataset is limited to human SNPs, and you know the list of SNPs, I would advise taking a look at the dedicated <a href="https://api.ncbi.nlm.nih.gov/variation/v0/" rel="nofollow noreferrer">NCBI Variation Services</a>.  This would be one request for each SNP, but if you fire off 1-2 per second, I think you'll be ok.</p>
  <p>For example, for rs1490381980, you could try something like:</p>
  <pre><code>curl -X GET 'https://api.ncbi.nlm.nih.gov/variation/v0/refsnp/1490381980' \
     | jq '.primary_snapshot_data.placements_with_allele[] | &quot;\(.seq_id) \(.alleles[0].allele.spdi.position)&quot;'
  </code></pre>
  <p>It would be better to query for the SNP and parse the JSON in python, but <code>jq</code> helps provide an idea of what is possible.</p>
  <p>Alternatively, you could download the JSON or VCF data from the <a href="https://ftp.ncbi.nih.gov/snp/latest_release/" rel="nofollow noreferrer">NCBI dbSNP FTP site</a>, and process out the information you need.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-09-29T20:56:42.570Z
Answers.LastActivityDate: 2020-09-29T20:56:42.570Z
Answers.UserDisplayName: Brad Holmes
Body: <p>So I have the following e-utils api-link:</p>
  <blockquote>
  <p><a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gene&amp;db=snp&amp;id=5726&amp;retmode=json" rel="nofollow noreferrer">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gene&amp;db=snp&amp;id=5726&amp;retmode=json</a></p>
  </blockquote>
  <p>it returns all the SNP-ids for the gene with the id 5726 as an example. Additionally to the SNP-ids I also need the SNP position and the genomic distance. Also I would need the chromosome but I could query that from the gene as well rather than for each SNP. Do you know how I can add all these informations to the resulting json/xml?</p>
  <p>The first one in the resulting list is the SNP with the id 1490381980. Further information about it can be found on dbSNP: <a href="https://www.ncbi.nlm.nih.gov/snp/?term=1490381980%5BUID%5D" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/snp/?term=1490381980%5BUID%5D</a></p>
  <p>I really want to avoid creating a request for each single SNP and would prefer to query everything at once. Due to the unavoidable performance-issues. The Tas2R38 doesn't have that many SNPs but there are other genes with way more.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-07-03T17:41:57.527Z
Comments.Text: Hi @cowboy_patrick could you plase state/clarify what you mean by "to query everything at once. Due to unavoidable performance issues.".
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-07-04T03:35:54.257Z
Comments.Text: It would be great if I could get all the SNPs and their positions with a single api-call for a specified gene. Instead of creating a call for each SNP on the variation services or something similar
Comments.UserDisplayName: Cowboy_Patrick
Tags: <snp><phylogenetics><api>
Title: e-utils api: get chromosome position for each snp on a gene
ThreadText: # e-utils api: get chromosome position for each snp on a gene
  
  (Asked by: username_0 on 2020-07-03)
  
  So I have the following e-utils api-link:
  
  > <https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gene&db=snp&id=5726&retmode=json>
  
  it returns all the SNP-ids for the gene with the id 5726 as an example. Additionally to the SNP-ids I also need the SNP position and the genomic distance. Also I would need the chromosome but I could query that from the gene as well rather than for each SNP. Do you know how I can add all these informations to the resulting json/xml?
  
  The first one in the resulting list is the SNP with the id 1490381980. Further information about it can be found on dbSNP: <https://www.ncbi.nlm.nih.gov/snp/?term=1490381980%5BUID%5D>
  
  I really want to avoid creating a request for each single SNP and would prefer to query everything at once. Due to the unavoidable performance-issues. The Tas2R38 doesn't have that many SNPs but there are other genes with way more.
  
  **Tags:** snp, phylogenetics, api
  
  > **Comments:**
  > **username_1**: Hi @username_0 could you plase state/clarify what you mean by "to query everything at once. Due to unavoidable performance issues.".  
  > **username_0**: It would be great if I could get all the SNPs and their positions with a single api-call for a specified gene. Instead of creating a call for each SNP on the variation services or something similar  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2020-09-29. Score: 2
  
  If your dataset is limited to human SNPs, and you know the list of SNPs, I would advise taking a look at the dedicated [NCBI Variation Services](https://api.ncbi.nlm.nih.gov/variation/v0/). This would be one request for each SNP, but if you fire off 1-2 per second, I think you'll be ok.
  
  For example, for rs1490381980, you could try something like:
  
  ```
  curl -X GET 'https://api.ncbi.nlm.nih.gov/variation/v0/refsnp/1490381980' \
     | jq '.primary_snapshot_data.placements_with_allele[] | "\(.seq_id) \(.alleles[0].allele.spdi.position)"'
  
  ```
  
  It would be better to query for the SNP and parse the JSON in python, but `jq` helps provide an idea of what is possible.
  
  Alternatively, you could download the JSON or VCF data from the [NCBI dbSNP FTP site](https://ftp.ncbi.nih.gov/snp/latest_release/), and process out the information you need.
  
  
  ---
  
  