Pleiotropic Expression Quantitative Trait Loci Are Enriched in Enhancers and Transcription Factor Binding Sites and Impact More Genes

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.