DOI: 10.25452/figshare.plus.27327684
title: iPSCORE QTL-GWAS Colocalizations

description: This directory contains two files from the results of performing Bayesian colocalization between iPSCORE quantitative trait loci (QTLs) and GWAS loci from 15 traits and diseases. Briefly, QTLs for three molecular phenotypes (gene expression [eQTLs], chromatin accessibility [caQTLs], and H3K27ac acetylation [haQTLs]) were identified in three tissues from the iPSCORE Collection; induced pluripotent stem cells (iPSCs), iPSC-derived cardiovascular progenitor cells (CVPCs), and iPSC-derived pancreatic progenitor cells (PPCs). To assess if these QTLs overlapped GWAS loci, we performed Bayesian colocalization, using the <i>coloc</i> R package (Giambartolomei et al 2014).The <i>GWAS_QTL_Colocalization_CredibleSets.txt.gz</i> file contains 32,343 SNPs in 99% credible sets from iPSCORE QTLs that colocalized with at least one GWAS loci. These SNPs were intersected with the TFBSs in the <i>Transcription Factor Binding Predictions</i> directory in this repository to identify motif-overlapping causal SNPs. The file contains columns for; <b>Tissue </b>the corresponding tissue, <b>Element_ID</b> the identifier for the molecular affected by the QTL, <b>Trait_Description</b> the description of the GWAS trait or disease, <b>Trait_ID</b> the identifier for the GWAS trait, <b>SNP_ID</b> the identifier of the SNP in the [<i>"VAR"</i>_<i>Chromosome_</i><i>Position_</i><i>ReferenceAllele_</i><i>Alternate</i>Allele] labeling convention, <b>PosteriorProbability</b> the posterior probability for the SNP, <b>QTL_Beta</b> the effect size of the QTL, <b>QTL_Pvalue</b> the P-value of the QTL, <b>QTL_SE</b> the standard error of the QTL, and <b>GWAS_Beta</b>, <b>GWAS_SE</b>, and <b>GWAS_Pvalue</b> the effect size, standard error and p-value of the SNP in the GWAS loci, respectively.The <i>GWAS_QTL_Colocalization_Summaries.txt.gz </i>file summarizes the QTL-GWAS colocalizations by reporting the SNP with the highest posterior probability for all 522,034 colocalizations. The file contains columns for: <b>Tissue </b>the corresponding tissue, <b>Element_ID</b> the identifier for the molecular affected by the QTL, <b>Cluster_ID</b> the identifier for QTL cluster, <b>Complexity</b> whether the QTL is "Complex" and affect multiple elements or "Singleton" and affects only one element, <b>QTL_Combo</b> the combination of molecular phenotypes that the QTL affects, <b>Representative</b> TRUE/FALSE whether the QTL signal was randomly selected to represent the QTL signal, <b>Colocalized </b>TRUE/FALSE based on if the QTL colocalized with the GWAS loci (PP.H4 &gt;= 0.8, QTL_Pvalue &lt; 5e-5, GWAS_Pvalue &lt; 5e-8, and Number of SNPs tested &gt;=50), <b>Trait_Description</b> the description of the GWAS trait or disease, <b>Trait_ID </b>the identifier for the GWAS trait or disease, <b>No_SNPs_Tested</b> the number of SNPs tested in the colocalization, <b>PP.H0.abf</b>, <b>PP.H1.abf</b>, <b>PP.H2.abf</b>, <b>PP.H3.abf</b>, <b>PP.H4.abf</b> the posterior probability for each of the 5 hypotheses from the coloc R package, <b>Likely_Model</b> the coloc hypothesis with the highest posterior probability, <b>Top_SNP_ID</b> the identifier of the SNP with the highest PP in the [<i>"VAR"</i>_<i>Chromosome_</i><i>Position_</i><i>ReferenceAllele_</i><i>Alternate</i>Allele] labeling convention, <b>TopSNP_PP</b> the posterior probability of the top SNP, <b>QTL_Beta</b>, <b>QTL_SE</b>, <b>QTL_Pvalue</b> the effect size, standard error, and p-value of the top SNP in the QTL, and <b>GWAS_Beta</b>, <b>GWAS_SE</b>, <b>GWAS_Pvalue </b>the effect size, standard error, and p-value of the top SNP in the GWAS locus.