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c-Myc. E2f1. 49. 3. 14.9. 2 c-Myc. Klf4. 33. 1. 15.7. 2 c-Myc n-Myc. 1246. 0. 300.0. 4. Ctcf. E2f1. 79. 6. 67.5. 3. Ctcf. Esrrb. 34. 57. 10.0. 3. Ctcf. Tcfcp2l1 22. 2. 8.4.

Table S6 All significant pairwise spatial binding constraints detected from mouse ES cell ChIP-Seq data TF1

TF2

c-Myc c-Myc c-Myc Ctcf Ctcf Ctcf E2f1 E2f1 E2f1 E2f1 Esrrb Esrrb Esrrb Esrrb Esrrb Esrrb Esrrb Klf4 Klf4 Klf4 Klf4 Klf4 Klf4 Klf4 Klf4 Klf4 Nanog Nanog Nanog Nanog Nanog Nanog Nanog Nr5a2 Nr5a2 Nr5a2 Oct4 P300 Smad1 Sox2 Sox2

E2f1 Klf4 n-Myc E2f1 Esrrb Tcfcp2l1 Ctcf Klf4 n-Myc Zfx Klf4 Nanog n-Myc Nr5a2 Oct4 Sox2 Tcfcp2l1 Ctcf Esrrb Nanog n-Myc Nr5a2 Oct4 Sox2 Tcfcp2l1 Zfx Klf4 Nr5a2 Oct4 P300 Smad1 Sox2 Tcfcp2l1 Sox2 Tcfcp2l1 Zfx Sox2 Sox2 Sox2 Smad1 Tcfcp2l1

Count at strongest spacing 49 33 1246 79 34 22 62 248 157 148 164 79 42 2352 30 76 316 24 166 93 72 33 20 119 119 66 95 35 276 48 43 1595 41 30 57 29 482 51 49 49 61

Distance of strongest spacing 3 1 0 6 57 2 6 3 1 6 31 58 23 1 24 56 10 9 31 24 1 30 27 25 41 5 24 57 7 2 1 1 65 58 11 0 6 1 0 0 66

Max -log10(p-value)

# Significant Positions

14.9 15.7 300.0 67.5 10.0 8.4 46.4 195.8 93.9 61.4 115.5 74.6 9.6 300.0 10.8 62.4 259.4 15.0 117.7 141.0 45.5 31.7 9.0 186.2 94.6 26.2 144.4 41.7 300.0 102.0 97.2 300.0 34.8 32.7 58.5 26.8 300.0 99.6 108.8 111.3 58.2

2 2 4 3 3 1 3 2 7 2 43 3 1 4 10 25 85 2 40 1 4 3 1 6 4 1 1 5 12 1 1 3 4 4 2 1 50 1 1 1 8

43