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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/

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  • $\begingroup$ Good you've got the answer. FYI @CristianRiccio you'll find you can now upvote because you've >20 rep (hint, hint :-) ). $\endgroup$
    – M__
    Commented Mar 7, 2023 at 16:42

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They are using hg19.

I found this by simply going to "Browse" 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:

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.

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