GTEx eQTL Scraper

GTEx eQTL Scraper

Scrape GTEx eQTL data for any gene and tissue, up to a million associations per run. Every result includes the variant ID, p-value, normalized effect size, and gene symbol. No API key required. Export to CSV, JSON, Excel, or XML.

The GTEx Portal's web interface limits you to browsing one gene-tissue pair at a time and offers no bulk export. This Actor reads the public GTEx eQTL API directly, so you can collect variant-gene associations filtered by Gencode ID and tissue site in a single run. It returns a flat dataset ready for downstream analysis.

Who uses it	What they scrape GTEx Portal for
Bioinformaticians	Pull eQTL summary statistics for colocalization and Mendelian randomization studies.
Genetic epidemiologists	Retrieve tissue-specific eQTLs to annotate GWAS loci.
Computational biologists	Build gene regulatory network models with GTEx variant effects.
Pharma researchers	Identify functional variants that regulate drug target genes in disease-relevant tissues.

What it does

This Actor collects GTEx eQTL associations by Gencode gene ID and tissue site, and returns each variant-gene pair as a flat row.

• 🧬 Gene-centric queries: supply a Gencode ID to fetch all eQTLs for that gene across the selected tissue.
• 🫁 Tissue-specific filtering: restrict results to a single tissue site like Whole_Blood, Liver, or Brain_Cortex.
• 📊 Scalable collection: set a maxItems limit up to 1,000,000 to control run size and cost.
• 📄 Flat structured output: each row is one variant-gene pair with p-value, effect size, and gene symbol.

Results export to CSV, JSON, Excel, or XML, or straight from the API.

What you can do with GTEx Portal data

🧬 Annotate GWAS hits with tissue eQTLs.

A statistical geneticist feeds a list of Gencode IDs for genes near GWAS lead SNPs and pulls their Whole_Blood eQTLs to check for colocalization.

🧪 Build a drug-target eQTL catalog.

A pharma researcher scrapes eQTLs for PCSK9 in Liver to find regulatory variants that may influence LDL cholesterol levels.

🧠 Compare eQTL effects across tissues.

A computational biologist runs the same gene against Brain_Cortex and Whole_Blood to see how variant effects differ by tissue context.

📈 Feed eQTL priors into fine-mapping tools.

A bioinformatician collects eQTL summary statistics for a locus and formats the output for use with SuSiE or FINEMAP.

Why choose this scraper

	What you get
Bulk eQTL retrieval	Collect thousands of associations in one run instead of clicking through the web portal.
Fixed schema	Every row has the same columns: variant ID, p-value, NES, tissue, and gene symbol.
No API key	Reads the public GTEx API endpoint with no registration or authentication.
Analysis-ready export	Download results as CSV, JSON, Excel, or XML for direct use in R or Python.

How it compares

No other Store actor targets GTEx Portal the same way, so the honest comparison is with the alternatives teams actually weigh.

	GTEx eQTL Scraper	Build it in-house	By hand
Setup	Run it now, zero config	Days of engineering	None, but hours per pull
When GTEx Portal changes	Maintained for you	You fix it	You re-learn the page
Proxies, retries, anti-bot	Built in	Your problem	Browser only
Output	Fixed JSON schema, CSV/Excel export	Whatever you build	Copy-paste
Cost	Pay per result	Engineering time	Analyst hours

Configure the run

Drive the Actor with a Gencode gene ID and a tissue site name, alone or together, and the maxItems cap stops the run once enough eQTLs are collected. The Input tab lists every parameter.

A first run with the defaults:

{
  "maxItems": 10,
  "gencodeId": "ENSG00000169174.10",
  "tissueSiteDetailId": "Whole_Blood"
}

A larger pull:

{
  "maxItems": 200,
  "gencodeId": "ENSG00000169174.10",
  "tissueSiteDetailId": "Whole_Blood"
}

Pricing

Pay-per-result: $0.0085 per result collected. You pay only for the results written to your dataset.

Results collected	Approximate cost
100 results	$0.85
1,000 results	$8.50
10,000 results	$85.00

New Apify accounts start with $5 in free credit.

Free users

Free-plan runs return up to 10 results as a preview. Upgrade your Apify plan to collect up to 1,000,000 results per run.

Run it

1. Create a free Apify account with $5 in credit.
2. Open the GTEx eQTL Scraper.
3. Set your inputs and any filters, then click Start.
4. Export the results as CSV, Excel, JSON, or XML from the Dataset tab.

Run it programmatically through the Apify API (run-sync-get-dataset-items) or the ApifyClient for JavaScript and Python.

Use with AI agents (MCP)

Give an AI agent live access to GTEx Portal through the Model Context Protocol. Add the Actor to Claude, Cursor, or any MCP client:

$claude mcp add --transport http apify "https://mcp.apify.com?tools=parseforge/gtex-eqtl-scraper"

Then prompt it in plain language to run the scraper and read back the results.

Troubleshooting

Why am I getting no results?

Check that your Gencode ID includes the version suffix (e.g., .10) and that the tissue name matches the GTEx portal exactly, including underscores. Some gene-tissue pairs have no significant eQTLs.

The run fails with an error about the Gencode ID.

Ensure the ID is a valid Ensembl Gencode identifier. Try looking up your gene on the GTEx Portal and copying the ID directly from the browser address bar.

I get fewer results than my maxItems setting.

The Actor stops when the GTEx API returns no more significant eQTLs for that gene-tissue pair. The number of real associations is often smaller than the cap you set.

The tissue name I used is not recognized.

Tissue names are case-sensitive and use underscores. Visit the GTEx Portal tissue browse page and copy the exact tissueSiteDetailId value from the URL or dropdown.

FAQ

Question	Answer
What is a Gencode ID and where do I find one?	A Gencode ID is a stable gene identifier like ENSG00000169174.10. You can find them on the Gencode website or by searching your gene symbol on the GTEx Portal and copying the ID from the URL.
Which tissue names can I use?	Use the GTEx tissue site detail names exactly as they appear on the portal, such as Whole_Blood, Liver, Brain_Cortex, or Adipose_Subcutaneous. The input accepts any valid GTEx tissue string.
Does this Actor require a GTEx API key or login?	No. It reads the public GTEx eQTL REST API endpoint, which does not require authentication or an API key.
What fields does each output row contain?	Each row includes the variant ID, p-value, normalized effect size (NES), tissue site detail ID, Gencode gene ID, and gene symbol. The exact field list is shown in the dataset preview after a test run.
Can I scrape eQTLs for multiple genes in one run?	The input accepts one Gencode ID per run. To collect eQTLs for multiple genes, run the Actor once per gene, or use an Apify task array to trigger parallel runs.
How do I limit the number of results?	Set the maxItems field to an integer between 1 and 1,000,000. The Actor stops fetching once that many eQTL associations have been collected.
What export formats are supported?	You can export the dataset as CSV, JSON, Excel, or XML from the Apify platform after the run completes.
Is the data from GTEx version 8?	Yes, the public GTEx eQTL API serves the version 8 release data, which includes 49 tissues and the full set of significant variant-gene pairs.

Related actors

Browse the full ParseForge collection for more scrapers.

🆘 Need help? Email parseforge@protonmail.com with your run ID, your input, and what you expected.

⚠️ Disclaimer. This Actor is unofficial and is not affiliated with, endorsed by, or sponsored by Broad Institute of MIT and Harvard. It collects only publicly available data. You are responsible for using the collected data in compliance with the source's terms of service and applicable data-protection laws, including GDPR, CCPA, and PIPL. Do not use it to collect personal data unlawfully.