is a Data Source.
The eQTLGen Consortium conducts large-scale meta-analyses of expression quantitative trait loci (eQTLs) in blood samples to investigate the genetic architecture of gene expression and understand the genetic underpinnings of complex traits. Phase I analyzed 31,684 blood and PBMC samples from 37 cohorts, identifying thousands of cis-eQTLs, trans-eQTLs, and expression quantitative trait score (eQTS) associations. The consortium also includes a single-cell eQTLGen project. Phase II is expanding to genome-wide eQTL meta-analysis across even more blood-based cohorts. The resulting summary statistics provide a valuable resource for interpreting genome-wide association studies (GWAS), developing novel methods, and understanding molecular mechanisms of complex traits.
genomics, biological systems
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| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| eqtlgen.cis_eqtl_significant | Significant cis-eQTLs | 2019-12-11-cis-eQTLsFDR0.05-ProbeLevel-CohortInfoRemoved-BonferroniAdded.txt.gz (307.8 MB) | Product | tsv | Significant cis-eQTL associations fro... |
| eqtlgen.cis_eqtl_full | Full cis-eQTL Summary Statistics | 2019-12-11-cis-eQTLsFDR-ProbeLevel-CohortInfoRemoved-BonferroniAdded.txt.gz (3.6 GB) | Product | tsv | Full cis-eQTL summary statistics from... |
| eqtlgen.trans_eqtl_significant | Significant trans-eQTLs | 2018-09-04-trans-eQTLsFDR0.05-CohortInfoRemoved-BonferroniAdded.txt.gz (1.8 MB) | Product | tsv | Significant trans-eQTL associations f... |
| eqtlgen.trans_eqtl_full | Full trans-eQTL Summary Statistics | 2018-09-04-trans-eQTLsFDR-CohortInfoRemoved-BonferroniAdded.txt.gz (5.7 GB) | Product | tsv | Full trans-eQTL summary statistics fr... |
| eqtlgen.cis_eqtl_smr | SMR-formatted cis-eQTLs | cis-eQTL-SMR_20191212.tar.gz (1.3 GB) | Product | txt | cis-eQTL results formatted for Summar... |
| eqtlgen.allele_frequencies | Allele Frequencies | 2018-07-18_SNP_AF_for_AlleleB_combined_allele_counts_and_MAF_pos_added.txt.gz (228.9 MB) | Product | tsv | Allele frequencies for all tested SNP... |
| eqtlgen.phase1_browser | eQTLGen Phase I Browser | phase1.html | GraphicalInterface | http | Web interface for browsing significan... |
| eqtlgen.phase2_cookbook | eQTLGen Phase II Cookbook | eQTLGen-p2-cookbook.html | DocumentationProduct | http | Analysis cookbook and documentation f... |
| eqtlgen.sc_website | Single-cell eQTLGen Website | sc | GraphicalInterface | http | Website for the single-cell eQTLGen p... |
| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| epigraphdb.graph | EpiGraphDB Graph Database | graph-database | GraphProduct | neo4j | Integrated graph knowledge base combi... |
The eQTLGen Consortium is a collaborative effort to map the genetic architecture of blood gene expression through large-scale meta-analyses of expression quantitative trait loci (eQTLs). By harmonizing data from dozens of cohorts worldwide, the consortium provides highly powered detection of genetic effects on gene expression.
The summary statistics and analysis resources enable researchers to interpret GWAS findings, prioritize candidate genes, and understand molecular mechanisms underlying complex traits.
Created: September 03, 2025 | Last modified: October 21, 2025