Genomic DNA sequences from sites in physical proximity can be inserted at SpCas9 cut sites. (a) All insertions longer than or equal to 25 bases were identified and plotted. (b) Number of cut sites with at least one (aligned) long insertion was plotted against the insertion length. (c) Average similarity of the insertion location within the same cut site and gene was compared across donors. This was also performed on a shuffled set of insertions as a control. Average genomic distance quantifies the distance between the donor sites of the long insertions that originate from the same chromosome. Bootstrap mean and standard deviation of 1,521 sites is shown in the table. (d) Quantification of the HiC contact data to the long insertions. Neighboring blocks as well as a randomly selected block were used as controls. The HiC block size was also varied. Bootstrap mean and standard error of the mean are shown in the table. (e) HiC chromosome contact maps were directly compared to the aligned long insertions. P value is computed using t-test.