What You Call "Coding Region" On Ensembl Variation
Hello, and I have a question regarding GWAS catalog (https://www.ebi.ac.uk/gwas/ ). From this dataset, How can I distinguish those SNPs are in coding region or non-coding region?
I mean that Is it ok in general to understand that variants in "coding-region" is equal to variants in orange regions of the picture from: http://asia.ensembl.org/info/genome/variation/predicted_data.html?
(i.e. You guys refer to variants in coding regions as :synonymous, missense, inframe insertion, inframe deletion, stop gained, frameshift, coding sequence variant?)
Thanks in advance.
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The variants are classified in GWAS catalog under the "Functional class" column and you have already found the help page for those classes. Is there an unanswered question here?
i am sorry, but i want to know the common sense of what you guys scientist call coding regions, is my understanding collect, you think?
Assuming you are not from a biology background, coding means that the DNA directly codes for a protein, essentially the DNA is transcribed and translated to protein.
(Ignoring the semantic discussion of "is UTR coding or not" for the sake of simplicity)
From original post:
Ensembl glossary defines CDS/coding sequence as
Variants in red box will have an effect (not always deleterious) on the encoded protein. The 4 effects above your red box would also be included in this class.
Thank you very much for your kind answer. I finally come to understand, but not fully, and from your view I might be asking a stupid question... The pic attached is I think correct in context of "variants that directly affect encoded protein".