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Humans demonstrate a structural elaboration of this niche with a rhombic lip subventricular zone (RL-SVZ). Disruption of this zone causes cerebellar malformations and tumors, yet its gene regulatory networks are poorly understood. We present a predicted gene regulatory network for the human RL inferred from epigenomic maps of the developing human cerebellum. We generated DNA methylomes from microdissected mid-gestation human RL ventricular zone (RL-VZ) and RL-SVZ (\n                    <jats:italic>N<\/jats:italic>\n                    \u2009=\u20099; 15\u201316 post-conception weeks) using low-input Enzymatic MethylSeq, and profiled histone marks of active promoters and enhancers in whole fetal cerebellum (\n                    <jats:italic>N<\/jats:italic>\n                    \u2009=\u20096; 14 and 18 weeks). Transition from RL-VZ to RL-SVZ is accompanied by widespread hypomethylation, including 9,855 differentially methylated regions (DMRs) enriched for binding sites of ATOH1, NEUROD1\/2, and HMGA1. Of these, 88.9% are hypomethylated in RL-SVZ, enriched in active enhancers and human accelerated regions, and depleted at promoters. By integrating DMRs with bulk tissue histone maps as well as single-cell chromatin accessibility and transcriptomic maps of the mid-gestation cerebellum, we inferred over 100,000 transcription factor\u2013enhancer\u2013gene links. Twenty-five DMRs overlap human accelerated regions near genes implicated in intellectual disability, autism spectrum disorder, and neurological deficits. DMRs are also enriched in copy-number aberrations in medulloblastoma, with ~\u200925% overlapping known aberrant regions, nominating disrupted promoters and enhancers. These data provide a framework for interpreting non-coding variation in human cerebellar development and disease.\n                  <\/jats:p>","DOI":"10.1007\/s12311-026-02057-4","type":"journal-article","created":{"date-parts":[[2026,7,21]],"date-time":"2026-07-21T06:29:11Z","timestamp":1784615351000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Differentially Methylated Regions in Human Rhombic Lip Compartments Are Enriched in Putative Active Enhancers, Human Accelerated Regions, and Medulloblastoma Copy Number Aberrations"],"prefix":"10.1007","volume":"25","author":[{"given":"Xinghan","family":"Sun","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Soumya","family":"Menon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul","family":"Wambo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ilinca","family":"Lungu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"name":"Birth Defects Research Laboratory","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kimberly A.","family":"Aldinger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1048-581X","authenticated-orcid":false,"given":"Shraddha","family":"Pai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,7,21]]},"reference":[{"key":"2057_CR1","doi-asserted-by":"publisher","first-page":"789","DOI":"10.1007\/s12311-015-0724-2","volume":"15","author":"K Leto","year":"2016","unstructured":"Leto K, et al. 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