Divergent patterns in gene expression play an essential role in the development of new traits between species. Accordingly, evolutionary changes in the cis-regulatory elements that cause gene expression differences occur more quickly than changes in protein-coding genes. Individual cis-regulatory elements undergo turnover and are frequently under selection between primates, and mutations in cis-regulatory elements can fine-tune a response to the environment by adjusting quantitative traits and their tissue specificity. The goal of this work is to further understand the tuning of gene regulation between primate species and within populations and what functional consequences there may be. Transcription factors are a primary determinant of regulatory interactions and therefore changes in transcription factor binding sites often contribute to changes in gene regulation. In order to determine how transcription factor binding patterns are evolutionary constrained in different tissues among humans, we developed a machine learning algorithm, dTOX, to predict transcription factor occupancy patterns based on DNase-I-seq, and used it to create an atlas of transcription factor binding across over a hundred human tissues. We found evidence of different evolutionary rates in the binding sites occupied by transcription factors among tissues, specifically between embryonic and adult tissues. Our results show that evolution in transcription factor binding mirrors the tissue-driven model of protein-coding gene evolution. By closely examining examples of cis-regulatory changes that contribute to a measurable difference in a trait in primate species, we can further understand the mechanisms of evolutionary change. We use the differential expression and regulation of the anthrax toxin receptor, ANTXR2, as a case study to understand how natural selection, the environment, and the regulatory landscape have contributed to a functional difference in the immune system of primates. We found evidence of a change in the cis-regulatory landscape of ANTXR2, signatures of selection between human populations, and population-specific polymorphisms that may contribute to differences in sensitivity to anthrax disease. Our results demonstrate how a regulatory change that was likely influenced by historical host-pathogen interactions has had lasting effects on immunity today both between species and within human populations.