Answers.Body: <p>I would run them through the <a href="http://www.ensembl.org/info/docs/tools/vep/index.html" rel="nofollow noreferrer">Ensembl VEP</a>, which will tell you which genes they hit and the effect they have on them. Then I would filter by consequence "mature_miRNA_variant", which will find you all the variants in your file that fall in the mature miRNAs. Or you could filter instead by the gene biotype "miRNA" which will tell you if the variants fall anywhere in the miRNAs (which will include the full stem loop structure). I would then export the list of miRNAs and try to find out about their targets using <a href="http://www.mirbase.org/" rel="nofollow noreferrer">miRbase</a>.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-07-23T08:04:50.023Z
Answers.LastActivityDate: 2018-07-23T08:04:50.023Z
Answers.UserDisplayName: Emily_Ensembl
Body: <p>I have 3 exomes results (VCF files), I would like to study variants (SNP, INDEL) that can affect the miRNAs, which are related to a complex disease (Schizophrenia). What is the best way to assess the effects of variants on miRNAs and how can I link between the damaged miRNAs and Schizophrenia. Can I find a help or advice please? </p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-07-23T10:47:56.507Z
Comments.Text: I assume that you want a bioinformatician approach, not an experimental one, and that depends on the data you have (or you can obtain). For instance, how do you measure the damaged miRNAs? What data do you already have?
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-07-24T10:48:41.440Z
Comments.Text: Do you want effects on miRNAs, or effects on their targets?
Comments.UserDisplayName: Ian Sudbery
Tags: <sequence-annotation>
Title: Variants in Exome that affect miRNAs related to Schizophrenia
ThreadText: # Variants in Exome that affect miRNAs related to Schizophrenia
  
  (Asked by: username_0 on 2018-07-20)
  
  I have 3 exomes results (VCF files), I would like to study variants (SNP, INDEL) that can affect the miRNAs, which are related to a complex disease (Schizophrenia). What is the best way to assess the effects of variants on miRNAs and how can I link between the damaged miRNAs and Schizophrenia. Can I find a help or advice please?
  
  **Tags:** sequence-annotation
  
  > **Comments:**
  > **username_1**: I assume that you want a bioinformatician approach, not an experimental one, and that depends on the data you have (or you can obtain). For instance, how do you measure the damaged miRNAs? What data do you already have?  
  > **username_2**: Do you want effects on miRNAs, or effects on their targets?  
  
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  ## 1 answers
  
  ### Answer by username_3 on 2018-07-23. Score: 1
  
  I would run them through the [Ensembl VEP](http://www.ensembl.org/info/docs/tools/vep/index.html), which will tell you which genes they hit and the effect they have on them. Then I would filter by consequence "mature\_miRNA\_variant", which will find you all the variants in your file that fall in the mature miRNAs. Or you could filter instead by the gene biotype "miRNA" which will tell you if the variants fall anywhere in the miRNAs (which will include the full stem loop structure). I would then export the list of miRNAs and try to find out about their targets using [miRbase](http://www.mirbase.org/).
  
  
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