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Low\u2010frequency variants may account for some of the \u201cmissing\u201d heritability. Therefore, we scanned low\u2010frequency variants located within putative craniofacial enhancers to identify novel OFC risk variants and implicate new regulatory elements in OFC pathogenesis. Analyses were performed in a multiethnic sample of 1,995 cases of cleft lip with or without cleft palate (CL\/P), 221 cases with cleft palate (CP) only, and 1,576 unaffected controls. One hundred and nineteen putative craniofacial enhancers identified from ChIP\u2010Seq studies in craniofacial tissues or cell lines contained multiple low\u2010frequency (0.01\u20131%) variants, which we genotyped in participants using a custom Illumina panel. Two complementary statistical approaches, sequence kernel association test and combined multivariate and collapsing, were used to test association of the aggregated low\u2010frequency variants across each enhancer region with CL\/P and CP. We discovered a significant association between CP and a branchial arch enhancer near <jats:italic>FOXP1<\/jats:italic> (mm60; <jats:italic>p<\/jats:italic>\u2010value\u2009=\u2009.0002). Additionally, we observed a suggestive association between CL\/P and a forebrain enhancer near <jats:italic>FOXE1<\/jats:italic> (hs1717; <jats:italic>p<\/jats:italic>\u2010value\u2009=\u2009.001). These findings suggest that low\u2010frequency variants in craniofacial enhancer regions contribute to the complex etiology of nonsyndromic OFCs.<\/jats:p>","DOI":"10.1002\/ajmg.a.61002","type":"journal-article","created":{"date-parts":[[2018,12,24]],"date-time":"2018-12-24T14:39:09Z","timestamp":1545662349000},"page":"467-474","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":25,"title":["Association of low\u2010frequency genetic variants in regulatory regions with nonsyndromic orofacial clefts"],"prefix":"10.1002","volume":"179","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1897-1131","authenticated-orcid":false,"given":"John R.","family":"Shaffer","sequence":"first","affiliation":[{"name":"Center for Craniofacial and Dental Genetics, Department of Oral Biology School of Dental Medicine, University of Pittsburgh  Pittsburgh Pennsylvania"},{"name":"Department of Human Genetics Graduate School of Public Health, University of Pittsburgh  Pittsburgh Pennsylvania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jessica","family":"LeClair","sequence":"additional","affiliation":[{"name":"Department of Computational and Systems Biology School of Medicine, University of Pittsburgh  Pittsburgh Pennsylvania"},{"name":"Department of Biostatistics School of Public Health, Boston University  Boston Massachusetts"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jenna C.","family":"Carlson","sequence":"additional","affiliation":[{"name":"Center for Craniofacial and Dental Genetics, Department of Oral Biology School of Dental Medicine, University of Pittsburgh  Pittsburgh Pennsylvania"},{"name":"Department of Human Genetics Graduate School of Public Health, University of Pittsburgh  Pittsburgh Pennsylvania"},{"name":"Department of Biostatistics Graduate School of Public Health, University of Pittsburgh  Pittsburgh Pennsylvania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eleanor","family":"Feingold","sequence":"additional","affiliation":[{"name":"Department of Human Genetics Graduate School of Public Health, University of Pittsburgh  Pittsburgh Pennsylvania"},{"name":"Department of Biostatistics Graduate School of Public Health, University of Pittsburgh  Pittsburgh Pennsylvania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carmen J.","family":"Bux\u00f3","sequence":"additional","affiliation":[{"name":"Dental and Craniofacial Genomics Core School of Dental Medicine, University of Puerto Rico  San Juan Puerto Rico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kaare","family":"Christensen","sequence":"additional","affiliation":[{"name":"Department of Epidemiology Institute of Public Health, University of Southern Denmark  Odense Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Frederic W. 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