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4.1 years ago
u9001090
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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.
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.
All variants are relative to their reference sequence.
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).
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.
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).
Dear RamRS, thank you very much, your answers really helped.