DOI: 10.5281/zenodo.14064653
title: Pleiotropic Expression Quantitative Trait Loci Are Enriched in Enhancers and Transcription Factor Binding Sites and Impact More Genes

description: This dataset comprises two files that accompany the article (link to be added upon publication).

1. gwas2eqtl_colocalization_full.tar.gz

This file contains the complete colocalization dataset generated using the code from the following GitHub repository: gwas2eqtl. This dataset is used as input for the pleiotropic eQTL analysis available at gwas2eqtl_pleiotropy, which produces the figures in the article.

File structure:



.└── gwas417    └── coloc        ├── ebi-a-GCST000998        │   └── pval_5e-08        │       └── r2_0.1        │           └── kb_1000        │               └── window_1000000        │                   ├── Alasoo_2018_ge_macrophage_IFNg+Salmonella.tsv        │                   ├── Alasoo_2018_ge_macrophage_IFNg.tsv...


Each TSV file contains the following columns:



chrom    pos    rsid    ref    alt    eqtl_gene_id    gwas_beta    gwas_pval    gwas_id    eqtl_beta    eqtl_pval    eqtl_id    PP.H4.abf    SNP.PP.H4    nsnps    PP.H3.abf    PP.H2.abf    PP.H1.abf    PP.H0.abf    coloc_variant_id    coloc_region1    109272258    rs4970834    C    T    ENSG00000168765    -0.12874.25001047052626e-09    ebi-a-GCST000998    -0.250697    0.0893351    Alasoo_2018_ge_macrophage_IFNg+Salmonella    0.108283426725895    0.0520205502224409    6    0.000552728832012655    2.09397277427793e-07    0.890881419183881    0.000282215860934432    1_109279544_G_A    1:108779544-1097795431    109274968    rs12740374    G    T    ENSG00000168765    -0.103341    1.63998546891446e-09    ebi-a-GCST000998    -0.197397    0.172673Alasoo_2018_ge_macrophage_IFNg+Salmonella    0.108283426725895    0.0857585178966856    6    0.000552728832012655    2.09397277427793e-07    0.890881419183881    0.000282215860934432    1_109279544_G_A    1:108779544-1097795431    109275216    rs660240    T    C    ENSG00000168765    0.1044492.78997299740827e-09    ebi-a-GCST000998    0.214165    0.139318    Alasoo_2018_ge_macrophage_IFNg+Salmonella    0.108283426725895    0.0557749486050279    6    0.000552728832012655    2.09397277427793e-07    0.890881419183881    0.000282215860934432    1_109279544_G_A    1:108779544-1097795431    109275684    rs629301    G    T    ENSG00000168765    0.1054716.129993302249e-10    ebi-a-GCST000998    0.197397    0.172673    Alasoo_2018_ge_macrophage_IFNg+Salmonella    0.108283426725895    0.22229240584331    6    0.000552728832012655    2.09397277427793e-07    0.890881419183881    0.000282215860934432    1_109279544_G_A    1:108779544-1097795431    109278889    rs602633    T    G    ENSG00000168765    0.1034352.15998134341707e-09    ebi-a-GCST000998    0.226329    0.102673    Alasoo_2018_ge_macrophage_IFNg+Salmonella    0.108283426725895    0.0782482718431504    6    0.000552728832012655    2.09397277427793e-07    0.890881419183881    0.000282215860934432    1_109279544_G_A    1:108779544-109779543...


 

The dataset provides colocalization statistics for GWAS-eQTL pairs, including posterior probabilities and variant annotations.

2. gwas2eqtl0.1.3.tsv.gz

This file is a filtered version of the colocalization dataset, refined based on cutoffs of PP.H4.abf ≥ 0.75 and SNP.PP.H4 ≥ 0. This subset is utilized in the gwas2eqtl web application for data visualization.

Sample Columns:



chrom   pos19   pos38   cytoband        rsid    ref     alt     gwas_trait      gwas_class      gwas_beta       eqtl_gene_symbol        eqtl_beta       eqtl_id eqtl_gene_id    gwas_id gwas_pval       eqtl_pval          pp_h4_abf       snp_pp_h4       tophits_variant_id      nsnps1       1163804 1228424 1p36.33 rs7515488       C       T       Inflammatory bowel disease      Autoimmune dis. 0.0874308       ANKRD65 -0.175816       BrainSeq_ge_brain       ENSG00000235098 ebi-a-GCST003043           2.85292266979231e-10    0.000841046     0.978425254116226       6.18454060493069e-12    1_1312114_T_C   31       1163804 1228424 1p36.33 rs7515488       C       T       Inflammatory bowel disease      Autoimmune dis. 0.0874308       ANKRD65 -0.175816       BrainSeq_ge_brain       ENSG00000235098 ieu-a-294       2.85292266979231e-10       0.000841046     0.974019788384412       7.52286530905187e-12    1_1312114_T_C   41       1163804 1228424 1p36.33 rs7515488       C       T       Inflammatory bowel disease      Autoimmune dis. 0.0874308       ANKRD65 -0.293529       CommonMind_ge_DLPFC_naive       ENSG00000235098 ebi-a-GCST003043   2.85292266979231e-10    2.30452e-06     0.953333690803618       6.9758581004380506e-15  1_1312114_T_C   61       1163804 1228424 1p36.33 rs7515488       C       T       Inflammatory bowel disease      Autoimmune dis. 0.0874308       ANKRD65 -0.293529       CommonMind_ge_DLPFC_naive       ENSG00000235098 ieu-a-294          2.85292266979231e-10    2.30452e-06     0.951092499048109       7.0876793540547e-15     1_1312114_T_C   71       1163804 1228424 1p36.33 rs7515488       C       T       Inflammatory bowel disease      Autoimmune dis. 0.0874308       ANKRD65 -0.510549       FUSION_ge_adipose_naive ENSG00000235098 ebi-a-GCST003043           2.85292266979231e-10    1.2212e-06      0.974412793352836       1.70246427912903e-11    1_1312114_T_C   6


 

This filtered dataset focuses on high-confidence colocalization events for functional exploration of genetic associations and regulatory mechanisms.