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We used short- and long-read sequencing to generate a comprehensive variant catalog in Heterogeneous Stock (\n                  <jats:bold>HS<\/jats:bold>\n                  ) rats and performed joint cis-expression quantitative trait loci (\n                  <jats:bold>cis-eQTL<\/jats:bold>\n                  ) 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 (\n                  <jats:bold>LD<\/jats:bold>\n                  ). 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.\n                <\/jats:p>","DOI":"10.64898\/2026.09.10.750683","type":"posted-content","created":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T13:35:19Z","timestamp":1789565719000},"source":"Crossref","is-referenced-by-count":0,"title":["Point mutations and complex variants impact gene expression and addiction-related behaviors in Heterogeneous Stock rats"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6541-3418","authenticated-orcid":false,"given":"Denghui","family":"Chen","sequence":"first","affiliation":[{"name":"Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA 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