Answers.Body: <p>There are two types of data you can get from GTEx. The first is summary statistics, basically the slopes and p-values you see in the boxplot. You can also get expression levels for all genes measured in GTEx.</p>
  
  <p>However, in order to plot boxplot by yourself, you also need genotype data. This is not publicly available because of privacy issues. In order to get it, you have to apply to it on dbGaP. I think you can find relevant information on the GTEx website.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-03-29T19:59:10.770Z
Answers.LastActivityDate: 2020-03-30T02:46:44.063Z
Answers.LastEditDate: 2020-03-30T02:46:44.063Z
Answers.UserDisplayName: Phoenix Mu
Body: <p>I am new to the field of Bioinformatics. <a href="https://gtexportal.org/home/" rel="nofollow noreferrer">GTEx</a> database is great; I know how to check whether a SNP is eQtl <strong>with the online tools</strong> of GTEx. </p>
  
  <p>But my question is how to download the right data to draw a boxplot on my own. like this <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5567283/" rel="nofollow noreferrer">paper</a>:
  <a href="https://i.sstatic.net/zNkIm.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/zNkIm.png" alt="Figure 1 in this paper"></a></p>
  
  <p>Please help me . I have been stuck on this for many days.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-03-29T07:59:25.657Z
Comments.Text: I agree that GTEx is great, however for SNP variation however, I recommend using [gnomAD](https://gnomad.broadinstitute.org/) due to sheer number —and the high possibility that a reviewer will ask the same.
Comments.UserDisplayName: Matteo Ferla
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-03-29T08:03:24.277Z
Comments.Text: In recent years violin plots have taken over bloxplots as the common way to show such data —assuming few dataseries. Yes, five years ago showing a violin plot always required explaining but now the broader scientific community understands them.
Comments.UserDisplayName: Matteo Ferla
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-03-29T11:11:34.773Z
Comments.Text: @MatteoFerla THX for your note. I will go to learn how to use gnomAD. Would you please give me some hints that how to download the genotype data of a SNP (eg, sample 1 is AA ; sample 2 is AG, etc) from GTEx . I really want to know .
Comments.UserDisplayName: gong.y
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-03-29T11:29:43.033Z
Comments.Text: @MatteoFerla I want to perform eQTL analysis from GTEx. Help me please and that will save my life!
Comments.UserDisplayName: gong.y
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-03-30T02:18:43.600Z
Comments.Text: @ATpoint It‘s deleted. Thank you for your advice.
Comments.UserDisplayName: gong.y
Tags: <snp>
Title: How can I download the SNP genotyping information from GTEX?
ThreadText: # How can I download the SNP genotyping information from GTEX?
  
  (Asked by: username_0 on 2020-03-29)
  
  I am new to the field of Bioinformatics. [GTEx](https://gtexportal.org/home/) database is great; I know how to check whether a SNP is eQtl **with the online tools** of GTEx.
  
  But my question is how to download the right data to draw a boxplot on my own. like this [paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5567283/):
  [![Figure 1 in this paper](https://i.sstatic.net/zNkIm.png)](https://i.sstatic.net/zNkIm.png)
  
  Please help me . I have been stuck on this for many days.
  
  **Tags:** snp
  
  > **Comments:**
  > **username_1**: I agree that GTEx is great, however for SNP variation however, I recommend using [gnomAD](https://gnomad.broadinstitute.org/) due to sheer number —and the high possibility that a reviewer will ask the same.  
  > **username_1**: In recent years violin plots have taken over bloxplots as the common way to show such data —assuming few dataseries. Yes, five years ago showing a violin plot always required explaining but now the broader scientific community understands them.  
  > **username_0**: @username_1 THX for your note. I will go to learn how to use gnomAD. Would you please give me some hints that how to download the genotype data of a SNP (eg, sample 1 is AA ; sample 2 is AG, etc) from GTEx . I really want to know .  
  > **username_0**: @username_1 I want to perform eQTL analysis from GTEx. Help me please and that will save my life!  
  > **username_0**: @ATpoint It‘s deleted. Thank you for your advice.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2020-03-29. Score: 1 | Accepted answer
  
  There are two types of data you can get from GTEx. The first is summary statistics, basically the slopes and p-values you see in the boxplot. You can also get expression levels for all genes measured in GTEx.
  
  However, in order to plot boxplot by yourself, you also need genotype data. This is not publicly available because of privacy issues. In order to get it, you have to apply to it on dbGaP. I think you can find relevant information on the GTEx website.
  
  
  ---
  
  