Question: Why the same SNP show different alleles in different websites and papers (eg, rs560887)
0
gravatar for u9001090
7 weeks ago by
u90010900
u90010900 wrote:

Hi: Recently, I am looking for the information of rs560887. In NIH (pubmed), rs560887 showed Alleles T>C. However, some websites and papers showed rs560887 A/G (http://www.snpedia.com/index.php/Rs560887)!!? Why there are differences between them and what's allele variants are right for rs560887? Thanks.

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ADD COMMENTlink modified 5 weeks ago by Biostar ♦♦ 20 • written 7 weeks ago by u90010900
1
gravatar for RamRS
7 weeks ago by
RamRS27k
Houston, TX
RamRS27k wrote:

An A to G change on one strand is a T>C change on the other. If the gene is on a different strand, the change makes sense. Which paper is the source for this T>C notation?

ADD COMMENTlink written 7 weeks ago by RamRS27k

Thanks for your kindly reply. I didn't see any paper using the T>C notation. However, in my dataset (GWAS) and pubmed, they showed T>C notation. (http://www.ncbi.nlm.nih.gov/snp/rs560887) Most papers showed A/G. So, I don't know what should I mention when I am writing my manuscript, T>G (my GWAS) or A/G (follow other papers) or it doesn't matter? Thanks.

ADD REPLYlink written 7 weeks ago by u90010900

All variants are relative to their reference sequence.

and pubmed, they showed T>C notation (https://www.ncbi.nlm.nih.gov/snp/rs560887)

  1. If a pubmed paper showed A>G, please give us the link to the paper.
  2. The link you gave above is to the dbSNP entry, not to pubmed.

There might be reasons why the older papers went with A>G, and we cannot know those reasons unless we read the paper. Variant notations change a lot over time, so you should just go with the rsID and current HGVS notation (that includes a versioned reference sequence identifier).

ADD REPLYlink written 7 weeks ago by RamRS27k

Hi, I post the link of paper showing A>G here: https://reurl.cc/exWxrL. Page 17, Supplemental Table 3. The home page of this paper: Genome-Wide Screen for Metabolic Syndrome Thanks.

ADD REPLYlink written 6 weeks ago by u90010900

If you examine the table, they're picking two genes at that location: G6PC2 on the plus strand and ABCB11 on the minus strand. Perhaps their variant notation is with respect to ABCB11. The best way to find an answer would be to email the author(s).

ADD REPLYlink written 6 weeks ago by RamRS27k

Dear RamRS, thank you very much, your answers really helped.

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by u90010900
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