We sought to examine whether the non-canonical SMC protein Smchd1 plays a role in chromosome conformation. We used in situ Hi-C to analyse chromosome conformation changes upon deletion of the epigenetic regulator Smchd1 in female neural stem cells. In parallel, we analysed nucleosome accessibility using ATAC-seq, gene expression using RNA-seq, chromatin marks H3K27me3 and H3K27ac and Ctcf binding using ChIP-seq. We additionally analysed Smchd1 binding genome-wide using ChIP-seq. Together, we find that deletion of Smchd1 alters chromosome conformation at Smchd1 target genes including the inactive X chromosome, Hox genes and imprinted loc. Smchd1 deletion results in gain in Ctcf binding and activation of enhancers. We propose Smchd1 functions by limiting Ctcf-mediated chromosome looping. Overall design: n=2 Smchd1 GFP/GFP vs n=2 Smchd1+/+ female neural stem cell lines + Whole cell extract controls, to test binding of Smchd1 to the inactive X, using long sonication to release the inactive X heterochromatin. n=1 Smchd1GFP/GFP female + n=1 Smchd1 GFP/GFP male NSCs vs n=1 Smchd1+/+ female and n=1 Smchd1+/+ male neural stem cell lines plus whole cell extract controls, using MNase digestion for fragmentation, to assess autosomal binding of Smchd1.