{
  "abstract": "While various variants, including single nucleotide polymorphisms (SNPs), small insertions/deletions, short tandem repeats and structural variants, drive individual genetic differences, their influence on gene expression and complex traits remains unclear. We used short- and long-read sequencing to generate a comprehensive variant catalog in Heterogeneous Stock (HS) rats and performed joint cis-expression quantitative trait loci (cis-eQTL) mapping across five brain regions. We found that non-SNP variants accounted for over 50% of lead regulatory associations, many of which were poorly tagged by nearby SNPs using linkage disequilibrium (LD). Comparison between joint and SNP-only analyses showed that over 46% of shared eQTL genes had a non-SNP lead cis-eQTL, and fewer than half were in strong LD with the corresponding lead eSNP. Linking joint cis-eQTLs to complex trait associations identified mechanisms missed by SNP-only approaches, highlighting the importance of incorporating diverse variant types into genetic studies and providing a foundational resource for the HS rat community.",
  "abstract_shown": true,
  "affiliations": [
    "University of California San Diego"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 14,
  "authors": [
    {
      "name": "D. Chen"
    },
    {
      "name": "K. A. Cohen"
    },
    {
      "name": "K.-M. H. Nguyen"
    },
    {
      "name": "H. Ziaei Jam"
    },
    {
      "name": "R. J. Eveloff"
    },
    {
      "name": "Y. Wang"
    },
    {
      "name": "J. Guevara"
    },
    {
      "name": "T. Missfeldt Sanches"
    },
    {
      "name": "M. Mortazavi"
    },
    {
      "name": "D. Munro"
    },
    {
      "name": "O. Polesskaya"
    },
    {
      "name": "J. L. Sebat"
    },
    {
      "name": "M. Gymrek"
    },
    {
      "affs": [
        0
      ],
      "name": "A. A. Palmer"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/fqbg9ed22152f.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.09.10.750683",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.09.10.750683v1.full",
  "id": "fqbg9ed22152f",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.09.10.750683v1",
  "language": null,
  "licence": "CC-BY-NC-ND",
  "licence_label": "CC BY-NC-ND",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "genetics"
    ],
    [
      "openalex",
      "1311|Genetic Associations and Epidemiology"
    ]
  ],
  "openalex": "W7213286532",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.09.10.750683v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-10",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/fqbg9ed22152f.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:22:38Z",
      "native_id": "10.64898/2026.09.10.750683",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.09.10.750683v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:genetics",
      "subfield": "genetics-genomics"
    }
  ],
  "title": "Point mutations and complex variants impact gene expression and addiction-related behaviors in Heterogeneous Stock rats",
  "title_text": "Point mutations and complex variants impact gene expression and addiction-related behaviors in Heterogeneous Stock rats",
  "type": "preprint",
  "updated_at": "2026-10-30T12:22:38Z",
  "url": "https://research.draconitic.com/paper/fqbg9ed22152f",
  "venue": "bioRxiv",
  "versions": []
}