(A–C) Scatterplot comparison of distance-corrected interaction scores between (A) ES cells and NPCs, (B) ES and iPS cells and (C) NPCs and iPS cells. Thresholds are displayed as blue lines. For pairwise plots, cell type-specific, invariant and background interactions are represented by blue, grey and brown colored shading, respectively. (D) 3D scatterplot of distance-corrected interaction scores for cellular states in which both replicates cross the thresholds displayed in (A–C). Interaction classes are indicated by color (red, ES only; green, NPC only; orange, iPS only; gold, ES-NPC; purple, ES-iPS; blue, NPC-iPS; black, Background). Empirical false discovery rates computed from simulated data in (E–G) are reported for each classification. (E–G) Scatterplots of distance-corrected interaction scores from simulated replicates. Empirical false discovery rates were computed based on the number of interactions that cross pre-established thresholds in the simulated data versus the real data. (H) 3D scatterplot of distance-corrected interaction scores for simulated libraries that cross the thresholds displayed in (A–C, E–G). (I) Number of interactions called significant in each cell-type specific interaction class. (J) Schematic illustrating the 3D interaction behavior for each interaction class. (K–L) Zoomed-in heatmaps of distance-corrected interaction scores for specific (K) ES-iPS (purple class) and (L) ES only (red class) interactions. Classified interaction pixels are outlined in green. (M) Number of interactions called significant for each 3-D classification after clustering directly adjacent 4 kb bins. (N) Depiction of all interactions called as significant in the Sox2 region. Each interaction is outlined by the corresponding classification color.