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Background  Copy number variations (CNVs) are a significant source of genetic diversity and commonly found in mammalian genomes. We have generated a genome-wide CNV map for Cynomolgus monkeys ( Macaca fascicularis ). This crab-eating macaque is the closest animal model to humans that is used in biomedical research.    Results  We show that Cynomolgus monkey CNVs are in general much smaller in size than gene loci and are specific to the population of origin. Genome-wide expression data from five vitally important organs demonstrates that CNVs in close proximity to transcription start sites associate strongly with expression changes. Among these eQTL genes we find an overrepresentation of genes involved in metabolism, receptor activity, and transcription.    Conclusion  These results provide evidence that CNVs shape tissue transcriptomes in monkey populations, potentially offering an adaptive advantage. We suggest that this genetic diversity should be taken into account when using Cynomolgus macaques as models.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-017-3531-y) contains supplementary material, which is available to authorized users.

Diversity and regulatory impact of copy number variation in the primate Macaca fascicularis