Cis‐regulatory elements (CREs) play a pivotal role in spatiotemporal control of tissue‐specific gene expression, yet the molecular composition of the vast majority of CREs in native chromatin remains unknown. In this article, we describe the clustered regularly interspaced short palindromic repeats (CRISPR) affinity purification in situ of regulatory elements (CAPTURE) approach to simultaneously identify locus‐specific chromatin‐regulating protein complexes and long‐range DNA interactions. Using an in vivo biotinylated nuclease‐deficient Cas9 (dCas9) protein and programmable single guide RNAs (sgRNAs), this approach allows for high‐resolution and locus‐specific isolation of protein complexes and long‐range chromatin looping associated with single copy CREs in mammalian cells. Unbiased analysis of the compositional structure of developmentally regulated or disease‐associated CREs identifies new features of transcriptional regulation. Hence, CAPTURE provides a versatile platform to study genomic locus‐regulating chromatin composition in a mammalian genome.