Whole Genome Promoter-‐Proximal Regions

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Whole Genome Promoter-‐Proximal Regions TAF1 YY1 TBP E2F4 E2F6 ELF1 MAX POLR2A HMGN3 ZBTB7A CCNT2 EGR1 ETS1 SIN3A HDAC2 GABPA MXI1 MYC CHD2 IRF1 GTF2F1 THAP1 SP2 REST NRF1 USF1 FOS SP1 SRF SPI1 SIX5 CTCF RAD21 SMC3 CTCFL ZNF263 BCLAF1 TAF7 RDBP ZBTB33 BCL3 ATF3 USF2 NFE2 SETDB1 TRIM28 ZNF274 NR2C2 GATA1 GATA2 TAL1 EP300 SMARCA4 SMARCB1 SIRT6 JUNB JUND JUN FOSL1 MAFK CEBPB HDAC8 STAT1 STAT2 BDP1 POLR3A BRF1 GTF3C2 BRF2 TAF1 YY1 TBP E2F4 E2F6 ELF1 MAX POLR2A HMGN3 ZBTB7A CCNT2 EGR1 ETS1 SIN3A HDAC2 GABPA MXI1 MYC CHD2 IRF1 GTF2F1 THAP1 SP2 REST NRF1 USF1 FOS SP1 SRF SPI1 SIX5 CTCF RAD21 SMC3 CTCFL ZNF263 BCLAF1 TAF7 RDBP ZBTB33 BCL3 ATF3 USF2 NFE2 SETDB1 TRIM28 ZNF274 NR2C2 GATA1 GATA2 TAL1 EP300 SMARCA4 SMARCB1 SIRT6 JUNB JUND JUN FOSL1 MAFK CEBPB HDAC8 STAT1 STAT2 BDP1 POLR3A BRF1 GTF3C2 BRF2 TAF1 TAF1 TBP TBP YY1 YY1 ELF1 ELF1 MAX MAX E2F4 E2F4 E2F6 E2F6 IRF1 IRF1 EGR1 EGR1 ZBTB7A ZBTB7A ETS1 ETS1 SIN3A SIN3A CCNT2 CCNT2 HMGN3 HMGN3 HDAC2 HDAC2 GABPA GABPA CHD2 CHD2 POLR2A POLR2A GTF2F1 GTF2F1 MXI1 MXI1 MYC MYC THAP1 THAP1 SP1 SP1 SP2 SP2 NRF1 NRF1 REST REST SIX5 SIX5 B SRF SRF SPI1 SPI1 RAD21 RAD21 SMC3 SMC3 CTCF CTCF CTCFL CTCFL ZNF263 ZNF263 BCLAF1 BCLAF1 TAF7 TAF7 RDBP RDBP ZBTB33 ZBTB33 BCL3 BCL3 ATF3 ATF3 USF2 USF2 USF1 USF1 NFE2 NFE2 GATA1 GATA1 GATA2 GATA2 TAL1 TAL1 EP300 EP300 SMARCA4 SMARCA4 SMARCB1 SMARCB1 SIRT6 SIRT6 JUNB JUNB JUND JUND JUN JUN FOSL1 FOSL1 FOS FOS MAFK MAFK CEBPB CEBPB HDAC8 HDAC8 SETDB1 SETDB1 TRIM28 TRIM28 NR2C2 NR2C2 A ZNF274 ZNF274 STAT1 STAT1 STAT2 STAT2 BDP1 BDP1 POLR3A POLR3A BRF1 BRF1 GTF3C2 GTF3C2 BRF2 BRF2 Whole genome Promoter-proximal regions TAF1 YY1 TBP E2F4 E2F6 ELF1 MAX POLR2A HMGN3 ZBTB7A CCNT2 EGR1 ETS1 SIN3A HDAC2 GABPA MXI1 MYC CHD2 IRF1 GTF2F1 THAP1 SP2 REST NRF1 USF1 FOS SP1 SRF SPI1 SIX5 CTCF RAD21 SMC3 CTCFL ZNF263 BCLAF1 TAF7 RDBP ZBTB33 BCL3 ATF3 USF2 NFE2 SETDB1 TRIM28 ZNF274 NR2C2 GATA1 GATA2 TAL1 EP300 SMARCA4 SMARCB1 SIRT6 JUNB JUND JUN FOSL1 MAFK CEBPB HDAC8 STAT1 STAT2 BDP1 POLR3A BRF1 GTF3C2 BRF2 TAF1 TBP YY1 ELF1 MAX E2F4 E2F6 IRF1 Confidence EGR1 ZBTB7A ETS1 SIN3A High CCNT2 HMGN3 HDAC2 GABPA CHD2 POLR2A GTF2F1 MXI1 MYC THAP1 SP1 SP2 NRF1 REST SIX5 B SRF SPI1 RAD21 Medium SMC3 CTCF CTCFL ZNF263 BCLAF1 TAF7 RDBP ZBTB33 BCL3 ATF3 USF2 USF1 NFE2 GATA1 GATA2 TAL1 EP300 SMARCA4 Low SMARCB1 SIRT6 JUNB JUND 0 10 20 30 40 50 60 70 80 90 t100 JUN FOSL1 FOS MAFK Degree of co-association (z-score) CEBPB HDAC8 SETDB1 TRIM28 NR2C2 A ZNF274 STAT1 STAT2 BDP1 POLR3A BRF1 GTF3C2 BRF2 1 Intergenic regions HDAC2 GABPA MXI1 MYC CHD2 HDAC2 GABPA JUNB JUND JUN FOSL1 CHD2 EP300 SP1 HDAC2 NANOG Promoter- JUNB POLR2A HDAC2 proximal JUND GTF2F1 NANOG regions JUN MXI1 EP300 FOSL1 MYC SP1 HDAC2 GABPA MXI1 MYC CHD2 HDAC2 GABPA JUNB JUND JUN FOSL1 CHD2 EP300 SP1 HDAC2 NANOG JUNB POLR2A HDAC2 Intergenic JUND GTF2F1 NANOG regions JUN MXI1 EP300 FOSL1 MYC SP1 A (K562) B (K562) C (H1-hESC) 2 H1-hESC Promoter-proximal regions TAF1 TBP POLR2A TAF7 JUND YY1 SIN3A EGR1 NRF1 USF1 USF2 MAX ATF3 SRF SIX5 GABPA EP300 SP1 HDAC2 NANOG BCL11A POU5F1 RXRA CTBP2 SUZ12 TCF12 JUN RFX5 BCL3 CTCF RAD21 REST POLR2A TAF7 JUND TAF1 TBP YY1 SIN3A NRF1 EGR1 USF1 USF2 MAX GABPA ATF3 SRF SIX5 HDAC2 NANOG EP300 SP1 BCL11A POU5F1 RXRA JUN BCL3 CTCF RAD21 REST RFX5 CTBP2 SUZ12 TCF12 7 H1-hESC Intergenic regions TAF1 TBP POLR2A TAF7 JUND YY1 SIN3A EGR1 NRF1 USF1 USF2 MAX ATF3 SRF SIX5 GABPA EP300 SP1 HDAC2 NANOG BCL11A POU5F1 RXRA CTBP2 SUZ12 TCF12 JUN RFX5 BCL3 CTCF RAD21 REST POLR2A TAF7 JUND TAF1 TBP YY1 SIN3A NRF1 EGR1 USF1 USF2 MAX GABPA ATF3 SRF SIX5 HDAC2 NANOG EP300 SP1 BCL11A POU5F1 RXRA JUN BCL3 CTCF RAD21 REST RFX5 CTBP2 SUZ12 TCF12 8 K562 Whole-genome TAF1 YY1 TBP E2F4 E2F6 ELF1 MAX POLR2A HMGN3 ZBTB7A CCNT2 EGR1 ETS1 SIN3A HDAC2 GABPA MXI1 MYC CHD2 IRF1 GTF2F1 THAP1 SP2 REST NRF1 USF1 FOS SP1 SRF SPI1 SIX5 CTCF RAD21 SMC3 CTCFL ZNF263 BCLAF1 TAF7 RDBP ZBTB33 BCL3 ATF3 USF2 NFE2 SETDB1 TRIM28 ZNF274 NR2C2 GATA1 GATA2 TAL1 EP300 SMARCA4 SMARCB1 SIRT6 JUNB JUND JUN FOSL1 MAFK CEBPB HDAC8 STAT1 STAT2 BDP1 POLR3A BRF1 GTF3C2 BRF2 TAF1 TBP YY1 ELF1 MAX E2F4 E2F6 IRF1 EGR1 ZBTB7A ETS1 SIN3A CCNT2 HMGN3 HDAC2 GABPA CHD2 POLR2A GTF2F1 MXI1 MYC THAP1 SP1 SP2 NRF1 REST SIX5 SRF SPI1 RAD21 SMC3 CTCF CTCFL ZNF263 BCLAF1 TAF7 RDBP ZBTB33 BCL3 ATF3 USF2 USF1 NFE2 GATA1 GATA2 TAL1 EP300 SMARCA4 SMARCB1 SIRT6 JUNB JUND JUN FOSL1 FOS MAFK CEBPB HDAC8 SETDB1 TRIM28 NR2C2 ZNF274 STAT1 STAT2 BDP1 POLR3A BRF1 GTF3C2 BRF2 18 K562 Promoter-proximal regions TAF1 YY1 TBP E2F4 E2F6 ELF1 MAX POLR2A HMGN3 ZBTB7A CCNT2 EGR1 ETS1 SIN3A HDAC2 GABPA MXI1 MYC CHD2 IRF1 GTF2F1 THAP1 SP2 REST NRF1 USF1 FOS SP1 SRF SPI1 SIX5 CTCF RAD21 SMC3 CTCFL ZNF263 BCLAF1 TAF7 RDBP ZBTB33 BCL3 ATF3 USF2 NFE2 SETDB1 TRIM28 ZNF274 NR2C2 GATA1 GATA2 TAL1 EP300 SMARCA4 SMARCB1 SIRT6 JUNB JUND JUN FOSL1 MAFK CEBPB HDAC8 STAT1 STAT2 BDP1 POLR3A BRF1 GTF3C2 BRF2 TAF1 TBP YY1 ELF1 MAX E2F4 E2F6 IRF1 EGR1 ZBTB7A ETS1 SIN3A CCNT2 HMGN3 HDAC2 GABPA CHD2 POLR2A GTF2F1 MXI1 MYC THAP1 SP1 SP2 NRF1 REST SIX5 SRF SPI1 RAD21 SMC3 CTCF CTCFL ZNF263 BCLAF1 TAF7 RDBP ZBTB33 BCL3 ATF3 USF2 USF1 NFE2 GATA1 GATA2 TAL1 EP300 SMARCA4 SMARCB1 SIRT6 JUNB JUND JUN FOSL1 FOS MAFK CEBPB HDAC8 SETDB1 TRIM28 NR2C2 ZNF274 STAT1 STAT2 BDP1 POLR3A BRF1 GTF3C2 BRF2 19 K562 Intergenic regions TAF1 YY1 TBP E2F4 E2F6 ELF1 MAX POLR2A HMGN3 ZBTB7A CCNT2 EGR1 ETS1 SIN3A HDAC2 GABPA MXI1 MYC CHD2 IRF1 GTF2F1 THAP1 SP2 REST NRF1 USF1 FOS SP1 SRF SPI1 SIX5 CTCF RAD21 SMC3 CTCFL ZNF263 BCLAF1 TAF7 RDBP ZBTB33 BCL3 ATF3 USF2 NFE2 SETDB1 TRIM28 ZNF274 NR2C2 GATA1 GATA2 TAL1 EP300 SMARCA4 SMARCB1 SIRT6 JUNB JUND JUN FOSL1 MAFK CEBPB HDAC8 STAT1 STAT2 BDP1 POLR3A BRF1 GTF3C2 BRF2 TAF1 TBP YY1 ELF1 MAX E2F4 E2F6 IRF1 EGR1 ZBTB7A ETS1 SIN3A CCNT2 HMGN3 HDAC2 GABPA CHD2 POLR2A GTF2F1 MXI1 MYC THAP1 SP1 SP2 NRF1 REST SIX5 SRF SPI1 RAD21 SMC3 CTCF CTCFL ZNF263 BCLAF1 TAF7 RDBP ZBTB33 BCL3 ATF3 USF2 USF1 NFE2 GATA1 GATA2 TAL1 EP300 SMARCA4 SMARCB1 SIRT6 JUNB JUND JUN FOSL1 FOS MAFK CEBPB HDAC8 SETDB1 TRIM28 NR2C2 ZNF274 STAT1 STAT2 BDP1 POLR3A BRF1 GTF3C2 BRF2 20 .
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