Syntenic conservation is an effective strategy to identify evolutionarily conserved lncRNA orthologs. In this study, we identified a novel uncharacterized conserved lncRNA known asSyntenic Cardiovascular Conserved Region-Associated lncRNA-6 (scar-6)and functionally validated its role in coagulation and cardiovascular function. Precise editing of thescar-6lncRNA locus in zebrafish (scar-6gib007Δ12/Δ12) resulted in cranial hemorrhage and permeability defects. Further analysis, including overexpression, locus editing, and rescue experiments, provided compelling evidence for the critical role of thescar-6transcript in the coagulation process of zebrafish. Notably, rescue attempts were unsuccessful in mitigating cranial hemorrhage. Molecular investigation revealed that thescar-6RNA acts as an enhancer lncRNA (elncRNA), and controls the expression ofprozb, an inhibitor offactor Xa, through the enhancer element on its locus. Thescar-6locus actively suppresses the loop formation betweenprozbandscar-6sequences, facilitated by methylation of CpG island via theprdm14-PRC2complex, which is stabilized by thescar-6elncRNA transcript. Disruption of this mechanism inscar-6gib007Δ12/Δ12zebrafish led to impaired vascular function and subsequent hemorrhage. This was triggered by the activation of thePAR2receptor mediated by upregulation ofprozb, which in turn causedNF-κB-mediated endothelial cell activation. This study presents novel evidence for the multifaceted function of thescar-6locus, highlighting its crucial role in regulating the coagulation cascade geneprozband maintaining homeostasis and vascular function.SynopsisProZ-PZIis a natural inhibitor of activatedcoagulation factor X (F10)and plays a major role in maintaining hemostasis in-vivo. Here, the novel evolutionary syntenic conservedscar-6elncRNA locus is shown to regulateprozbexpression and control coagulation and vascular integrity in zebrafish.Thescar-6acts as an enhancer lncRNA (elncRNA). It controlsprozbexpression and modulates coagulation and vascular function in zebrafish.Thescar-6elncRNA stabilizes thePrdm14-PRC2complex binding toscar-6locus. This inhibitsprozb/scar-6looping via methylating the CpG island under wildtype conditions.Overexpressedprozbinscar-6edited animals activatesPAR2receptor, causing endothelial cell activation and vascular dysfunction.