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Blockchain technology has heralded a new era in digital innovation, revolutionizing our approach to designing and building distributed applications in the digital sphere. Blockchain technology operates as an immutable digital ledger, where each entry representing a digital transaction is indelible and cannot be altered once established. Initially designed as the fundamental framework for cryptocurrencies, blockchain has outgrown its original purpose, demonstrating significant potential in various industries and offering a variety of security and privacy features. Our study provides a thorough and current survey of blockchain applications, security, privacy concepts, primitives, and threat models. It stands out by concentrating on how blockchain technology intersects with emerging fields like IoT, EVs, FinTech, and healthcare systems in a single framework. To provide security and privacy features, blockchain systems employ different foundational notions and primitives while tackling diverse adversarial scenarios with various capabilities and goals. This study presents a fresh examination of the current state of applications, security and privacy notions and primitives, and threat models in blockchain systems. Additionally, this work highlights existing gaps in knowledge and outlines open questions, aiming to stimulate interest in further advancements in the field.