Data obtained from genomic research is stored in electronic form, on medical databases and bio-data-storage, where they are made available for queries and processing by many researchers. Recently, cloud computing is becoming a popular choice given its ability to offer and facilitate shared access to genomic data, and to make effective use of storage capabilities. Outsourcing the processing of genomic data over the cloud, especially that of patients’ sensitive data, entails certain confidentiality and security concerns. Various computing services must be used without endangering the individual's privacy. Although the exported data is easily protected by the transport layer security during transmission, a number of problems can still arise during the processing of the data. Storing unencrypted data in the cloud can lead to data leakage, while theoretically storing the data in encrypted form using the Private Information Retrieval (PIR) schemes causes the system to slow down during queries, limiting realworld effectiveness of PIR schemes. The present study aims to provide a more comprehensible compilation of the confidentiality of genomic data, by categorizing the solutions proposed in the literature, for confidentiality and security problems concerning the storage and query of genomic data in cloud environments. Unlike other studies, the attacks on genomic data and the proposal for this aggressive solution have been put together in this study. Furthermore, readers are informed about some open issues despite the proposed solutions.