Answers.Body: <p>They are using hg19.</p>
  <p>I found this by simply going to &quot;<a href="http://www.licpathway.net/VARAdb/Browse_all_variation.php?select=Chr::chr1" rel="nofollow noreferrer">Browse</a>&quot; then copying taking the first rsID in the list (rs1891805) and comparing the chromosomal position they give in VARAdb to what I see in dbSNP. VARAdb gives it as position 154904840 on chromosome 1 and <a href="https://www.ncbi.nlm.nih.gov/snp/rs1891805#variant_details" rel="nofollow noreferrer">dbSNP has</a>:</p>
  <pre><code>Sequence name       Change
  GRCh37.p13 chr 1    NC_000001.10:g.154904840T&gt;C
  GRCh38.p14 chr 1    NC_000001.11:g.154932364T&gt;C
  PMVK RefSeqGene     NG_053028.1:g.15287A&gt;G
  </code></pre>
  <p>GRCh37 is hg19, and GRCh38 is hg38. So, as you can see above, the position 154904840 is from hg19 and the hg38 position for this rsID is 154932364.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-03-07T14:47:58.037Z
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Answers.LastEditDate: 2023-03-07T14:58:22.277Z
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Body: <p>I am interested in annotating a list of variants using VARAdb. My coordinates use the GRCh38 (hg19) reference genome. However, I do not know which coordinate system VARAdb uses.</p>
  <p>A section of the VARAdb publication reads:
  &quot;GWAS have provided a large amount of data
  associating genetic variants with common phenotypes. We
  collected risk SNPs fromfive sources, including theNHGRI
  GWAS Catalog (29), GWASdb v2.0 (30), GAD (31), Johnson
  and O’Donnell (32), and GRASP v2.0 (33). Then, we
  filtered risk SNPs ofwhich ‘Variant ID’which are not ‘rsID’
  and <strong>transformed locations of risk SNPs from the GRCh38
  assembly version into the hg19 version in the GWAS Catalog</strong>.
  Finally, we obtained 1 515 001 risk SNPs associated
  with diseases, traits and phenotypes.&quot;</p>
  <p>which makes me think that they may be using the hg19 genome, but I am not sure.</p>
  <p>So, my question is:</p>
  <p>Which human reference genome version does VARAdb use?</p>
  <p>VARAdb database:
  <a href="http://www.licpathway.net/VARAdb/search.php" rel="nofollow noreferrer">http://www.licpathway.net/VARAdb/search.php</a></p>
  <p>VARAdb publication:
  <a href="https://pubmed.ncbi.nlm.nih.gov/33095866/" rel="nofollow noreferrer">https://pubmed.ncbi.nlm.nih.gov/33095866/</a></p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-03-07T16:42:25.407Z
Comments.Text: Good you've got the answer. FYI @CristianRiccio you'll find you can now upvote because you've >20 rep  (hint, hint :-) ).
Comments.UserDisplayName: M__
Tags: <sequence-annotation><database><reference-genome>
Title: Which human reference genome version does VARAdb use?
ThreadText: # Which human reference genome version does VARAdb use?
  
  (Asked by: username_0 on 2023-03-07)
  
  I am interested in annotating a list of variants using VARAdb. My coordinates use the GRCh38 (hg19) reference genome. However, I do not know which coordinate system VARAdb uses.
  
  A section of the VARAdb publication reads:
  "GWAS have provided a large amount of data
  associating genetic variants with common phenotypes. We
  collected risk SNPs fromfive sources, including theNHGRI
  GWAS Catalog (29), GWASdb v2.0 (30), GAD (31), Johnson
  and O’Donnell (32), and GRASP v2.0 (33). Then, we
  filtered risk SNPs ofwhich ‘Variant ID’which are not ‘rsID’
  and **transformed locations of risk SNPs from the GRCh38
  assembly version into the hg19 version in the GWAS Catalog**.
  Finally, we obtained 1 515 001 risk SNPs associated
  with diseases, traits and phenotypes."
  
  which makes me think that they may be using the hg19 genome, but I am not sure.
  
  So, my question is:
  
  Which human reference genome version does VARAdb use?
  
  VARAdb database:
  <http://www.licpathway.net/VARAdb/search.php>
  
  VARAdb publication:
  <https://pubmed.ncbi.nlm.nih.gov/33095866/>
  
  **Tags:** sequence-annotation, database, reference-genome
  
  > **Comments:**
  > **username_1**: Good you've got the answer. FYI @username_0 you'll find you can now upvote because you've >20 rep  (hint, hint :-) ).  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2023-03-07. Score: 3 | Accepted answer
  
  They are using hg19.
  
  I found this by simply going to "[Browse](http://www.licpathway.net/VARAdb/Browse_all_variation.php?select=Chr::chr1)" then copying taking the first rsID in the list (rs1891805) and comparing the chromosomal position they give in VARAdb to what I see in dbSNP. VARAdb gives it as position 154904840 on chromosome 1 and [dbSNP has](https://www.ncbi.nlm.nih.gov/snp/rs1891805#variant_details):
  
  ```
  Sequence name       Change
  GRCh37.p13 chr 1    NC_000001.10:g.154904840T>C
  GRCh38.p14 chr 1    NC_000001.11:g.154932364T>C
  PMVK RefSeqGene     NG_053028.1:g.15287A>G
  
  ```
  
  GRCh37 is hg19, and GRCh38 is hg38. So, as you can see above, the position 154904840 is from hg19 and the hg38 position for this rsID is 154932364.
  
  
  ---
  
  