The cost of sequencing is substantially decreasing with the rapid development of human genome sequencing technologies. The generated genome data are supporting various applications. The genome-wide associated analysis study between the single nucleotide polymorphisms and diseases may lead to more privacy breaches for considering single nucleotide polymorphisms linkage disequilibrium, because of sensitive information related to single nucleotide polymorphisms including individual identity, phenotype, and kinship. To this end, the matrix differential privacy preserving framework is proposed based on the correlated coefficient of single nucleotide polymorphisms linkage disequilibrium. Therefore, this framework can preserve privacy of genome data and single nucleotide polymorphisms linkage disequilibrium, while ensures a certain genome data utility. And it achieves the trade-off between genome data privacy and utility for single nucleotide polymorphisms linkage disequilibrium in genome-wide association studies. Furthermore, the proposed framework plays an important role for promoting genomic privacy preserving under single nucleotide polymorphisms linkage disequilibrium.