{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"medRxiv"}],"indexed":{"date-parts":[[2026,9,4]],"date-time":"2026-09-04T03:56:40Z","timestamp":1788494200714,"version":"build-2803163510"},"posted":{"date-parts":[[2026,2,5]]},"group-title":"Genetic and Genomic Medicine","reference-count":107,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,2,5]],"date-time":"2026-02-05T00:00:00Z","timestamp":1770249600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,2,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Many non-coding variants influence complex traits and diseases through gene regulation, yet the mechanisms linking these variants to downstream biology remain poorly understood. Here, we present\n                  <jats:italic>eQTLGen Phase 2<\/jats:italic>\n                  , a comprehensive genome-wide analysis of gene expression quantitative trait loci (eQTLs) in 43,301 blood samples from 52 datasets. Beyond local\n                  <jats:italic>cis<\/jats:italic>\n                  -effects, this sample size enabled the first systematic mapping of\n                  <jats:italic>trans<\/jats:italic>\n                  -eQTLs at scale. We identify\n                  <jats:italic>cis<\/jats:italic>\n                  -eQTLs for nearly all expressed genes (94.7%) and\n                  <jats:italic>trans<\/jats:italic>\n                  -eQTLs for over half (56.2%). Second, by colocalizing\n                  <jats:italic>cis<\/jats:italic>\n                  -eQTLs with\n                  <jats:italic>trans<\/jats:italic>\n                  -eQTLs, we infer a directed gene regulatory network comprising 47,554 directed gene regulatory relationships. These networks reveal how genetic perturbations in upstream regulators produce dose-dependent downstream effects, supported by Perturb-seq and ChIP-seq data. Third, integrating this network with 87 genome-wide association studies allows us to systematically prioritize trait-relevant pathways and candidate genes. Variants exerting both\n                  <jats:italic>cis<\/jats:italic>\n                  \u2013 and\n                  <jats:italic>trans<\/jats:italic>\n                  -effects are markedly more likely to colocalize with trait associations than\n                  <jats:italic>cis<\/jats:italic>\n                  -only variants, delineating a subset of functionally active\n                  <jats:italic>cis<\/jats:italic>\n                  -eQTLs from a large group with limited downstream impact. This distinction provides a conceptual framework for identifying regulatory variants that truly mediate complex trait biology. Together, these results provide a publicly available resource of\n                  <jats:italic>cis<\/jats:italic>\n                  \u2013 and\n                  <jats:italic>trans<\/jats:italic>\n                  -eQTLs and an in vivo scaffold for human gene-regulatory networks, elucidating how propagation of\n                  <jats:italic>cis<\/jats:italic>\n                  -effects modulates complex disease.\n                <\/jats:p>","DOI":"10.64898\/2026.02.04.26343575","type":"posted-content","created":{"date-parts":[[2026,2,6]],"date-time":"2026-02-06T01:15:28Z","timestamp":1770340528000},"source":"Crossref","is-referenced-by-count":5,"title":["<i>Trans<\/i>\n                  -eQTLs reveal the architecture of human gene regulatory networks"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8691-0053","authenticated-orcid":false,"given":"C.A. Robert","family":"Warmerdam","sequence":"first","affiliation":[{"name":"Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands"},{"name":"Oncode Institute, Utrecht, the Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7038-567X","authenticated-orcid":false,"given":"Harm-Jan","family":"Westra","sequence":"additional","affiliation":[{"name":"Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands"},{"name":"Oncode Institute, Utrecht, the Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8898-8484","authenticated-orcid":false,"given":"Adriaan","family":"van der Graaf","sequence":"additional","affiliation":[{"name":"Department of Computational Biology, University of Lausanne, Lausanne, Switzerland"},{"name":"Swiss Institute of Bioinformatics, Lausanne, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8431-3180","authenticated-orcid":false,"given":"Marc Jan","family":"Bonder","sequence":"additional","affiliation":[{"name":"Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands"},{"name":"Oncode Institute, Utrecht, the Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5654-3966","authenticated-orcid":false,"given":"Patrick","family":"Deelen","sequence":"additional","affiliation":[{"name":"Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands"},{"name":"Oncode Institute, Utrecht, the Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0441-0309","authenticated-orcid":false,"given":"Tijs","family":"van Lieshout","sequence":"additional","affiliation":[{"name":"Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands"},{"name":"Oncode Institute, Utrecht, the Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anke Jannie","family":"Landman","sequence":"additional","affiliation":[{"name":"Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-6108-411X","authenticated-orcid":false,"given":"Mihkel","family":"Jesse","sequence":"additional","affiliation":[{"name":"Institute of Computer Science, University of Tartu, Tartu, Estonia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benjamin J.","family":"Strober","sequence":"additional","affiliation":[{"name":"Computational Health Informatics Program, Boston Children\u2019s Hospital, Boston, MA, 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