In this study, we identified several lncRNAs (AL355488.1, FENDRR, LINC00922, TPT1-AS1, PXN-AS1, AC107464.3, AC107375.1, C18orf65, LINC00210, KIF25-AS1, and AL138899.1), which had all been rarely reported in NSCL/P and not the causative genes for cleft lip with or without cleft palate (CL/P), Moreover, we preliminarily substantiated the regulatory roles of lncRNAs FENDRR and TPT1-AS1 in HEPM cells and HOK cells. Here, TPT1 is linked to cleft lip.