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Cohesin protein complex controls chromosome structure and is important in a variety of biological processes. The mechanism by which cohesion shapes local chromosome structure and gene expression are not fully understood in addition to whether or not they have phenotypes and contribute to disease. To investigate molecular and cellular consequences, CRISPR/Cas9 edits were introduced to murine embryonic stem cells. Edited cells were seeded on a CellRaft Array and scanned using the AIR System to identify GFP positive and/or mCherry positive cells. Individual colonies were expanded into clonal cell lines, screened for genome edits by PCR and Sanger Sequencing, and cryogenically stored. This study provided a functional comparison of cohesion variants found in cancer within an isogenic system, revealing the relative roles of various cohesion perturbations on gene expression and maintenance of cellular identity.