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\u03b3) and structural forms within 17q21.31 were identified and analyzed for their association with PSP.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We found that the copy number of \u03b3 was associated with increased PSP risk (odds ratio [OR]\u2009=\u20091.10, <jats:italic>P<\/jats:italic>\u2009=\u20090.0018). From H1\u03b21\u03b31 (OR\u2009=\u20091.21) and H1\u03b22\u03b31 (OR\u2009=\u20091.24) to H1\u03b21\u03b34 (OR\u2009=\u20091.57), structural forms of H1 with additional copies of \u03b3 displayed a higher risk for PSP. The frequency of the risk sub\u2010haplotype H1c rises from 1% in individuals with two \u03b3 copies to 88% in those with eight copies. Additionally, \u03b3 duplication up\u2010regulates expression of <jats:italic>ARL17B<\/jats:italic>, <jats:italic>LRRC37A<\/jats:italic>\/<jats:italic>LRRC37A2<\/jats:italic>, and <jats:italic>NSFP1<\/jats:italic>, while down\u2010regulating <jats:italic>KANSL1<\/jats:italic>. Single\u2010nucleus RNA\u2010seq of the dorsolateral prefrontal cortex analysis reveals \u03b3 duplication primarily up\u2010regulates <jats:italic>LRRC37A<\/jats:italic>\/<jats:italic>LRRC37A2<\/jats:italic> in neuronal cells.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>The copy number of \u03b3 is associated with the risk of PSP after adjusting for H1\/H2, indicating that the complex structure at 17q21.31 is an important consideration when evaluating the genetic risk of PSP. \u00a9 2025 The Author(s). <jats:italic>Movement Disorders<\/jats:italic> published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.<\/jats:p><\/jats:sec>","DOI":"10.1002\/mds.30150","type":"journal-article","created":{"date-parts":[[2025,3,12]],"date-time":"2025-03-12T00:29:20Z","timestamp":1741739360000},"page":"950-961","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Copy Number Variation and Haplotype Analysis of <scp>17q21.31<\/scp> Reveals Increased Risk Associated with Progressive Supranuclear Palsy and Gene Expression Changes in Neuronal Cells"],"prefix":"10.1002","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4043-5060","authenticated-orcid":false,"given":"Hui","family":"Wang","sequence":"first","affiliation":[{"name":"Department of Pathology and Laboratory Medicine, Perelman School of Medicine University of Pennsylvania  Philadelphia Pennsylvania USA"},{"name":"Penn Neurodegeneration Genomics Center, Perelman School of Medicine University of Pennsylvania  Philadelphia Pennsylvania USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9225-9874","authenticated-orcid":false,"given":"Timothy S.","family":"Chang","sequence":"additional","affiliation":[{"name":"Movement Disorders Programs, Department of Neurology, David Geffen School of Medicine University of California Los Angeles  Los Angeles California USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5334-1306","authenticated-orcid":false,"given":"Beth A.","family":"Dombroski","sequence":"additional","affiliation":[{"name":"Department of Pathology and Laboratory Medicine, Perelman School of Medicine University of Pennsylvania  Philadelphia Pennsylvania USA"},{"name":"Penn Neurodegeneration Genomics Center, Perelman School of Medicine University of Pennsylvania  Philadelphia Pennsylvania USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-0046-0313","authenticated-orcid":false,"given":"Po\u2010Liang","family":"Cheng","sequence":"additional","affiliation":[{"name":"Department of Pathology and Laboratory Medicine, Perelman School of Medicine University of Pennsylvania  Philadelphia Pennsylvania USA"},{"name":"Penn Neurodegeneration Genomics Center, Perelman School of Medicine University of Pennsylvania  Philadelphia Pennsylvania USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9968-9754","authenticated-orcid":false,"given":"Ya\u2010Qin","family":"Si","sequence":"additional","affiliation":[{"name":"Bioinformatics Research Center North Carolina State University  Raleigh North Carolina USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5703-7208","authenticated-orcid":false,"given":"Albert","family":"Tucci","sequence":"additional","affiliation":[{"name":"Bioinformatics Research Center North Carolina State University  Raleigh North Carolina USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vishakha","family":"Patil","sequence":"additional","affiliation":[{"name":"Movement Disorders Programs, Department of Neurology, David Geffen School of Medicine University of California Los Angeles  Los Angeles California USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leopoldo","family":"Valiente\u2010Banuet","sequence":"additional","affiliation":[{"name":"Movement Disorders Programs, Department of Neurology, David Geffen School of Medicine University of California Los Angeles  Los Angeles California USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1949-4074","authenticated-orcid":false,"given":"Chong","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Computer and Information Sciences, College of Science and Technology Temple University  Philadelphia Pennsylvania USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6955-7278","authenticated-orcid":false,"given":"Kurt","family":"Farrell","sequence":"additional","affiliation":[{"name":"Department of Pathology, Department of Artificial Intelligence &amp; Human Health, Nash Family, Department of Neuroscience, Ronald M. 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