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Epidermal growth factor receptor (EGFR) was reportedly involved in its biological establishment and regulation of cell migration during the embryonic stage.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>We selected a super pathway of endocytic trafficking of EGFR and investigated the associations of single\u2010nucleotide polymorphisms (SNPs) in the super pathway with the risk of NSCL\/P by analyzing our published genome\u2010wide association study (GWAS) data from 504 NSCL\/P individuals and 455 controls. After the false discovery rate (FDR) control, we conducted linkage disequilibrium (LD) analyses and conditional regression analyses to obtain independent lead SNPs. We performed LD analyses between the lead SNPs and the reported SNPs to find novel ones from our study. We annotated the lead SNPs and investigated their mapped genes in silico.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>A total of 82 SNPs showed a statistical association with the risk of NSCL\/P after FDR control. They contained three reported SNPs which were g.117068049G&gt;A (rs7078160), g.117086783C&gt;G (rs10886040), and g.117101266G&gt;T (rs17095681). Four independent lead SNPs were obtained, including g.116979803\u00a0T&gt;C (rs1905539) and g.117037960A&gt;G (rs7902502) at 10q25.3, g.35720163G&gt;C (rs75656820) at 17q12, and g.156864512G&gt;A (rs1800877) at 1q23.1. Three of them were in low LD (<jats:italic>r<\/jats:italic><jats:sup>2<\/jats:sup>\u00a0&lt;\u00a00.5) with the reported SNPs except g.117037960A&gt;G (rs7902502), so these three were newly identified. Lead SNPs were mapped to three genes: <jats:italic>SHTN1<\/jats:italic>,<jats:italic> AP2B1,<\/jats:italic> and <jats:italic>NTRK1<\/jats:italic>. The three genes were relatively more highly expressed in the human craniofacial region and in the proximal maxillary location during the craniofacial development stage of the embryonic mouse.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>Our results suggested that <jats:italic>SHTN1<\/jats:italic>,<jats:italic> AP2B1,<\/jats:italic> and <jats:italic>NTRK1<\/jats:italic> might be associated with the development of NSCL\/P.<\/jats:p><\/jats:sec>","DOI":"10.1002\/mgg3.497","type":"journal-article","created":{"date-parts":[[2018,11,9]],"date-time":"2018-11-09T04:49:03Z","timestamp":1541738943000},"page":"1157-1167","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":19,"title":["Associations of genetic variants in endocytic trafficking of epidermal growth factor receptor super pathway with risk of nonsyndromic cleft lip with or without cleft palate"],"prefix":"10.1002","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2458-0380","authenticated-orcid":false,"given":"Bing","family":"Li","sequence":"first","affiliation":[{"name":"Department of Burns and Plastic Surgery, The Drum Tower Clinical Medical College Nanjing Medical University Nanjing China"},{"name":"Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology Nanjing Medical University Nanjing China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lan","family":"Ma","sequence":"additional","affiliation":[{"name":"Jiangsu Key Laboratory of Oral Diseases Nanjing Medical University Nanjing China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chi","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Orthodontics, Affiliated Hospital of Stomatology  Nanjing Medical University Nanjing China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhixuan","family":"Zhou","sequence":"additional","affiliation":[{"name":"Department of Polyclinic, Affiliated Hospital of Stomatology Nanjing Medical University Nanjing China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hua","family":"Yuan","sequence":"additional","affiliation":[{"name":"Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology Nanjing Medical University Nanjing China"},{"name":"Jiangsu Key Laboratory of Oral Diseases Nanjing Medical University Nanjing China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hongbing","family":"Jiang","sequence":"additional","affiliation":[{"name":"Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology Nanjing Medical University Nanjing China"},{"name":"Jiangsu Key Laboratory of Oral Diseases Nanjing Medical University Nanjing 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