Query some information about eqtl from GTEx API

This is a simple and convenient way to get some information about certain eqtls from GTEx API. But it may not be a good way to do big query because it’s not so fast.

Open a python notebook and load some packages

import requests
import json
import pandas as pd 
import time # if you want to measure the query speed

Get gene/tissue/variant info

gencode = "ENSG00000116127.17"
gene_name = "ALMS1"
tissue = "Heart_Left_Ventricle" # provide an exmple

Query the portal and get the result

gene_eqtls = requests.get('https://gtexportal.org/rest/v1/association/singleTissueEqtl', params = {"gencodeId" : gencode,"tissueSiteDetailId" : tissue, "datasetId" : "gtex_v8", "variantId" : 'chr2_73325414_G_A_b38'})

data = json.loads(gene_eqtls.text)

The result should be like:

{'singleTissueEqtl': [{'chromosome': 'chr2',
   'datasetId': 'gtex_v8',
   'gencodeId': 'ENSG00000116127.17',
   'geneSymbol': 'ALMS1',
   'geneSymbolUpper': 'ALMS1',
   'nes': 0.18502,
   'pValue': 1.1244e-05,
   'pos': 73325414,
   'snpId': 'rs7573275',
   'tissueSiteDetailId': 'Heart_Left_Ventricle',
   'variantId': 'chr2_73325414_G_A_b38'}]}

For some datasets like singleTissueEqtl with URL https://gtexportal.org/rest/v1/association/singleTissueEqtl, we can ask multiple variants with a single query. For example, we want effect sizes of two variants in a certain tissue.

gencode = "ENSG00000227232.5"
tissue = "Lung"
variantId = ("chr1_665098_G_A_b38","chr1_88794_T_A_b38")

test = requests.get('https://gtexportal.org/rest/v1/association/singleTissueEqtl', 
                   params = {"gencodeId" : gencode,"tissueSiteDetailId" : tissue, "datasetId" : "gtex_v8", "variantId" : variantId})

data_test = json.loads(test.text)

for i in range(len(data_test['singleTissueEqtl'])):

The result:


For some other dataset like dyneqtl with the URL https://gtexportal.org/rest/v1/association/dyneqtl, we can’t ask multiple variants/genes/tissues with a single query.


Text and figures are licensed under Creative Commons Attribution CC BY 4.0. The source code is licensed under MIT.

Suggest changes

If you find any mistakes (including typos) or want to suggest changes, please feel free to edit the source file of this page on Github and create a pull request.


For attribution, please cite this work as

Charles Zhou (2022). How to query eqtl info from GTEx API (a simple way). ImLab Notes. /post/2022/05/22/how-to-query-eqtl-info-from-gtex-api-a-simple-way/

BibTeX citation

  title = "How to query eqtl info from GTEx API (a simple way)",
  author = "Charles Zhou",
  year = "2022",
  journal = "ImLab Notes",
  note = "/post/2022/05/22/how-to-query-eqtl-info-from-gtex-api-a-simple-way/"