We had similar findings (not emphasized in the publication) in our study of variant characterization at TNFAIP3. Different "monocyte" cell lines looked very distinct. "B cell" lines looked very distinct. Cell lines are often bad proxies for primary cells in terms of gene regulation.
Carl de Boer
Deciphering the limitations of immortalized hepatocyte cell lines for the study of liver cis-regulatory elements https://www.biorxiv.org/content/10.64898/2026.06.05.730479v1
