Answers.Body: <p>You just searched for <code>X[Chromosome]</code>, you didn't specify a species. Presumably, your dataset comes from a specific species, so you should limit your search to that species. For instance, for human, you can search dbSNP for <a href="https://www.ncbi.nlm.nih.gov/snp/?term=X%5BChromosome%5D%20human%5Borganism%5D" rel="nofollow noreferrer"><code>X[Chromosome] human[organism]</code></a>. Then, click on the <code>send to</code> link at the top left and download the data: </p>
  
  <p><a href="https://i.sstatic.net/BvgJG.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/BvgJG.png" alt="dbSNP screenshot"></a></p>
  
  <p>This is veeeeeery slow, however. I suggest that you instead download the data for chrX from dbSNP's FTP site (this assumes your species of interest is human): <a href="ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/chr_rpts/chr_X.txt.gz" rel="nofollow noreferrer">ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/chr_rpts/chr_X.txt.gz</a></p>
  
  <p>Once you have this file, you can use it to filter your dataset:</p>
  
  <ol>
  <li><p>Collect all rsIDs from the file:</p>
  
  <pre><code>zcat chr_X.txt.gz | awk '/^[0-9]/{print "rs"$1}' &gt; chrX.rsIDs
  </code></pre></li>
  <li><p>Filter your dataset.</p>
  
  <p>You haven't shown the format of your dataset, so if it is just a list of rsIDs like this:</p>
  
  <pre><code>$ cat dataset
  rs77669712
  rs199706910
  rs2799940 
  rs12205639
  rs10958205
  rs200778574
  </code></pre>
  
  <p>You can remove any that are on chrX with:</p>
  
  <pre><code>$ grep -vxFf chrX.rsIDs dataset 
  rs77669712
  rs199706910
  rs12205639
  rs10958205
  rs200778574
  </code></pre>
  
  <p>That will print all rsIDs from the text file <code>dataset</code> that are not also in the text file <code>chrX.rsIDs</code>. Note the <code>-x</code> option for <code>grep</code> which tells it to only consider matches that cover the entire line. This ensures that <code>rs1234</code> is not removed when you're looking for <code>rs123</code>. </p></li>
  </ol>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-01-12T10:25:10.107Z
Answers.LastActivityDate: 2018-01-14T11:35:57.607Z
Answers.LastEditDate: 2018-01-14T11:35:57.607Z
Answers.UserDisplayName: terdon
Body: <p>Where can I find a list of SNP rs IDs that belong to the X chromosome? </p>
  
  <p>I'm trying to exclude the SNPs on X-chromosome in a data set, but I don't know where these SNPs come from. </p>
  
  <p>I tried to use <a href="https://www.ncbi.nlm.nih.gov/snp?term=X%5BChromosome%5D" rel="nofollow noreferrer">dbSNP</a> to search, it returns 26933249 SNPs, but the webpage seems to refuse me to download the information. </p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-01-12T05:49:32.580Z
Comments.Text: Have you tried the send to option in the top right corner, just below the search bar?
Comments.UserDisplayName: arup
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-01-12T09:16:35.363Z
Comments.Text: In what species? Your search didn't specify a species, are you really interested in rsIDs from *any* species?
Comments.UserDisplayName: terdon
Tags: <snp><phylogenetics>
Title: Where can I find a list of SNP rs IDs that belong to the X chromosome?
ThreadText: # Where can I find a list of SNP rs IDs that belong to the X chromosome?
  
  (Asked by: username_0 on 2018-01-12)
  
  Where can I find a list of SNP rs IDs that belong to the X chromosome?
  
  I'm trying to exclude the SNPs on X-chromosome in a data set, but I don't know where these SNPs come from.
  
  I tried to use [dbSNP](https://www.ncbi.nlm.nih.gov/snp?term=X%5BChromosome%5D) to search, it returns 26933249 SNPs, but the webpage seems to refuse me to download the information.
  
  **Tags:** snp, phylogenetics
  
  > **Comments:**
  > **username_1**: Have you tried the send to option in the top right corner, just below the search bar?  
  > **username_2**: In what species? Your search didn't specify a species, are you really interested in rsIDs from *any* species?  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2018-01-12. Score: 6 | Accepted answer
  
  You just searched for `X[Chromosome]`, you didn't specify a species. Presumably, your dataset comes from a specific species, so you should limit your search to that species. For instance, for human, you can search dbSNP for [`X[Chromosome] human[organism]`](https://www.ncbi.nlm.nih.gov/snp/?term=X%5BChromosome%5D%20human%5Borganism%5D). Then, click on the `send to` link at the top left and download the data:
  
  [![dbSNP screenshot](https://i.sstatic.net/BvgJG.png)](https://i.sstatic.net/BvgJG.png)
  
  This is veeeeeery slow, however. I suggest that you instead download the data for chrX from dbSNP's FTP site (this assumes your species of interest is human): <ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/chr_rpts/chr_X.txt.gz>
  
  Once you have this file, you can use it to filter your dataset:
  
  1. Collect all rsIDs from the file:
  
     ```
     zcat chr_X.txt.gz | awk '/^[0-9]/{print "rs"$1}' > chrX.rsIDs
  
     ```
  2. Filter your dataset.
  
     You haven't shown the format of your dataset, so if it is just a list of rsIDs like this:
  
     ```
     $ cat dataset
     rs77669712
     rs199706910
     rs2799940 
     rs12205639
     rs10958205
     rs200778574
  
     ```
  
     You can remove any that are on chrX with:
  
     ```
     $ grep -vxFf chrX.rsIDs dataset 
     rs77669712
     rs199706910
     rs12205639
     rs10958205
     rs200778574
  
     ```
  
     That will print all rsIDs from the text file `dataset` that are not also in the text file `chrX.rsIDs`. Note the `-x` option for `grep` which tells it to only consider matches that cover the entire line. This ensures that `rs1234` is not removed when you're looking for `rs123`.
  
  
  ---
  
  