Question

Same rs ID mapping to different genes

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2.5 years ago

elielsonveloso • 0

Hello, Biostars community!

I did a VEP annotation analysis and noticed that the same rs ID maps to different genes. My output looks like this. I noticed that for HLA-DQB2 there is no distance value, so the SNP is actually inside of HLA-DQB2. Meanwhile, the SNP is 12256 nucleotides upstream from MIR3135B. Based on that, can I rule out MIR3135B from further analysis ? I would appreciate any insights on that! VEP Output

GeneID SNPID • 543 views

ADD COMMENT • link updated 2.5 years ago by ATpoint 85k • written 2.5 years ago by elielsonveloso • 0

score 0 · Answer 1 · 2022-06-09

That depends entirely on what the variant is and what you want to analyse. If you are after gene variants then it probably does not affect that miR directly. If the mutation overlaps a regulatory element that controls that miR then it might be relevant. There is not a simple rule for this, in biology there unfortunately never is, everything is complex and complicated and you have to make a decision based on the question you want to answer.