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 Indonesia is the world's fourth most crowded nation, host to striking degrees of human assorted variety, provincial examples of admixture, and shifting degrees of introgression from the two Neanderthals and Denisovans. Be that as it may, it has been to a great extent rejected from the human genomics sequencing blast of the most recent decade. To fill in as a benchmark dataset of sub-atomic phenotypes over the locale, we created genome-wide CpG methylation and quality articulation estimations in more than 100 people from three areas that catch the major genomic and topographical tomahawks of assorted variety over the Indonesian archipelago. Examining between-and inside island contrasts, we find up to 10.55% of tried qualities are differentially communicated between the islands of Sumba and New Guinea. Variety in quality articulation is firmly connected with DNA methylation, with articulation levels of 9.80% of qualities relating with close by advertiser CpG methylation, and a significant number of these qualities being differentially communicated between islands. Qualities recognized in our differential articulation and methylation examinations are advanced in pathways associated with insusceptibility, featuring Indonesia's tropical job as a wellspring of irresistible malady decent variety and the solid specific weights these infections have applied on people. At last, we distinguish powerful inside island variety in DNA methylation and quality articulation, likely determined by fine-scale ecological contrasts across inspecting destinations. Together, these outcomes unequivocally recommend complex connections between DNA methylation, interpretation, ancient hominin introgression and invulnerability, all mutually formed by nature. This has suggestions for the use of genomic medication, both in fundamentally understudied Indonesia and internationally, and will permit a superior comprehension of the associating jobs of genomic and ecological elements molding sub-atomic and complex phenotypes