Recently, CRISPR/Cas9 genome editing has been employed to introduce short insertions and deletions and identify transcriptional regulatory elements in a high-throughput fashion. However, scalability of these methods is limited by the number of targeted perturbations that can be introduced. Further, existing approaches neglected the issue of cis- and trans-regulation. Here we report a highly scalable method, Cis Regulatory Element Scan by Tiling-deletion and sequencing (CREST-seq), for unbiased discovery and functional assessment of cis regulatory sequences in the genome with improved coverage and sensitivity comparing to existing single sgRNA screen approach.