Table S9. Predicted enhancers in BMP4 differentiated ES cells. Coordinates are in hg17. ENCODE region Position Chr ENr122 59798651 chr18 ENr211 25834378 chr16 ENr211 26108478 chr16 ENr211 26200778 chr16 ENr132 112354715 chr13 ENr132 112360615 chr13 ENr132 112405715 chr13 ENr132 112413815 chr13 ENr132 112415715 chr13 ENr132 112422515 chr13 ENr132 112431815 chr13 ENr132 112459315 chr13 ENr132 112483715 chr13 ENr132 112505815 chr13 ENr132 112596515 chr13 ENr132 112724915 chr13 ENr334 41448045 chr6 ENr334 41519545 chr6 ENr334 41541045 chr6 ENr334 41547745 chr6 ENr334 41564445 chr6 ENr334 41570445 chr6 ENr334 41580745 chr6 ENr334 41596345 chr6 ENr334 41645545 chr6 ENr334 41648045 chr6 ENr334 41654445 chr6 ENr334 41656345 chr6 ENr334 41700145 chr6 ENr334 41721045 chr6 ENr334 41732345 chr6 ENr334 41799445 chr6 ENr334 41816045 chr6 ENr334 41824045 chr6 ENr334 41843345 chr6 ENm002 131359064 chr5 ENm002 131360664 chr5 ENm002 131366464 chr5 ENm002 131569764 chr5 ENm002 131589964 chr5 ENm002 131598564 chr5 ENm002 131622564 chr5 ENm002 131629164 chr5 ENm002 131659264 chr5 ENm002 131665464 chr5 ENm002 131685464 chr5 ENm002 131752164 chr5 ENm002 131760164 chr5 ENm002 131791864 chr5 ENm002 131801264 chr5 ENm002 131809064 chr5 ENm002 131828764 chr5 ENm002 131839264 chr5 ENm002 131841264 chr5 ENm002 132123764 chr5 ENm002 132135264 chr5 ENm002 132152164 chr5 ENm002 132164164 chr5 ENm002 132171664 chr5 ENm002 132203864 chr5 ENm010 27024511 chr7 ENm010 27026711 chr7 ENm010 27039511 chr7 ENm010 27063811 chr7 ENm010 27070411 chr7 ENm010 27119011 chr7 ENm010 27159911 chr7 ENm010 27186411 chr7 ENm010 27188211 chr7 ENr223 73876903 chr6 ENr223 73968703 chr6 ENr121 118186854 chr2 ENr121 118200854 chr2 ENr121 118244554 chr2 ENm009 5668546 chr11 ENm009 5702146 chr11 ENr331 220143201 chr2 ENr331 220150901 chr2 ENr331 220160401 chr2 ENr331 220190201 chr2 ENr331 220202401 chr2 ENr331 220211301 chr2 ENr331 220217101 chr2 ENr331 220251901 chr2 ENr331 220267801 chr2 ENr331 220335501 chr2 ENr331 220353801 chr2 ENr331 220372001 chr2 ENr331 220393101 chr2 ENr331 220418601 chr2 ENr331 220562101 chr2 ENr322 98572274 chr14 ENr322 98669774 chr14 ENr322 98714074 chr14 ENr322 98752374 chr14 ENr322 98754074 chr14 ENr322 98767174 chr14 ENr322 98769474 chr14 ENr322 98777974 chr14 ENr322 98798374 chr14 ENr322 98937774 chr14 ENr322 98949374 chr14 ENr133 39252417 chr21 ENr133 39282217 chr21 ENr133 39288517 chr21 ENr133 39299117 chr21 ENr133 39315217 chr21 ENr133 39323317 chr21 ENr133 39390217 chr21 ENr133 39391917 chr21 ENr133 39431917 chr21 ENr133 39454717 chr21 ENr133 39724517 chr21 ENr131 234665175 chr2 ENm004 30305158 chr22 ENm004 30322758 chr22 ENm004 30345358 chr22 ENm004 30771558 chr22 ENm004 30779758 chr22 ENm004 31252458 chr22 ENm004 31254158 chr22 ENm004 31260758 chr22 ENm004 31267158 chr22 ENm004 31276258 chr22 ENm004 31277858 chr22 ENm004 31325858 chr22 ENm004 31327458 chr22 ENm004 31337458 chr22 ENm004 31343758 chr22 ENm004 31352858 chr22 ENm004 31364958 chr22 ENm004 31370758 chr22 ENm004 31404658 chr22 ENm004 31419158 chr22 ENm004 31433258 chr22 ENm004 31434958 chr22 ENm004 31456058 chr22 ENm004 31466158 chr22 ENm004 31474258 chr22 ENm004 31485458 chr22 ENm004 31506258 chr22 ENm004 31538958 chr22 ENm004 31551658 chr22 ENm004 31560458 chr22 ENm004 31601758 chr22 ENm004 31671858 chr22 ENm004 31698558 chr22 ENm004 31707158 chr22 ENm004 31714858 chr22 ENm004 31750258 chr22 ENm013 89847590 chr7 ENm013 89853590 chr7 ENm013 89897690 chr7 ENm013 89935390 chr7 ENm013 89952090 chr7 ENm013 89981590 chr7 ENm013 90001090 chr7 ENm013 90090990 chr7 ENr312 130699748 chr11 ENr312 130798948 chr11 ENr312 130840148 chr11 ENr312 130846748 chr11 ENr312 130933348 chr11 ENr312 131032348 chr11 ENr312 131045048 chr11 ENr212 141891101 chr5 ENr212 141903201 chr5 ENr212 141910501 chr5 ENr212 141927101 chr5 ENr212 141950001 chr5 ENr212 141959201 chr5 ENr212 141966601 chr5 ENr212 141981501 chr5 ENr212 141986301 chr5 ENr212 141996801 chr5 ENr212 142004701 chr5 ENr212 142045501 chr5 ENr212 142057801 chr5 ENr212 142094501 chr5 ENr212 142144501 chr5 ENr212 142205501 chr5 ENr212 142243301 chr5 ENr212 142261201 chr5 ENr212 142342001 chr5 ENr323 108393947 chr6 ENr323 108400347 chr6 ENr323 108418947 chr6 ENr323 108518647 chr6 ENr323 108546847 chr6 ENr323 108594347 chr6 ENr323 108680047 chr6 ENr323 108681847 chr6 ENr323 108705847 chr6 ENm012 113649134 chr7 ENm012 113893434 chr7 ENm012 114070334 chr7 ENm012 114076734 chr7 ENm012 114163434 chr7 ENm012 114221234 chr7 ENm012 114237434 chr7 ENm012 114321934 chr7 ENm012 114459134 chr7 ENm012 114465334 chr7 ENr233 41596339 chr15 ENr233 41692639 chr15 ENr233 41747839 chr15 ENr233 41959339 chr15 ENr233 41981139 chr15 ENr233 41993139 chr15 ENr233 42000739 chr15 ENr233 42010939 chr15 ENr113 118700409 chr4 ENm006 152665495 chrX ENm006 152689295 chrX ENm006 152727295 chrX ENm006 152785995 chrX ENm006 152806095 chrX ENm006 152808395 chrX ENm006 152826695 chrX ENm006 152829595 chrX ENm006 152837795 chrX ENm006 152850495 chrX ENm006 153298095 chrX ENm006 153324795 chrX ENm006 153332595 chrX ENm006 153527095 chrX ENm006 153529195 chrX ENm006 153591595 chrX ENm006 153679795 chrX ENr213 23755982 chr18 ENr213 23898682 chr18 ENr213 23905582 chr18 ENr213 23912982 chr18 ENr213 23943482 chr18 ENr213 23949882 chr18 ENr213 23967782 chr18 ENr213 23969682 chr18 ENr213 23987182 chr18 ENr213 23993782 chr18 ENr213 23995882 chr18 ENm008 67251 chr16 ENm008 103351 chr16 ENm008 321551 chr16 ENm008 336051 chr16 ENm008 447451 chr16 ENm008 473751 chr16 ENm008 481951 chr16 ENr222 132447790 chr6 ENr222 132495090 chr6 ENr222 132695390 chr6 ENr321 118929271 chr8 ENr321 118976971 chr8 ENr321 118978771 chr8 ENr321 118993771 chr8 ENr321 119002371 chr8 ENr321 119008671 chr8 ENr321 119014871 chr8 ENr321 119022371 chr8 ENr321 119029371 chr8 ENr321 119038571 chr8 ENr321 119076471 chr8 ENr321 119086971 chr8 ENr321 119092871 chr8 ENr321 119100071 chr8 ENr321 119107871 chr8 ENr321 119116671 chr8 ENr321 119127671 chr8 ENr321 119155871 chr8 ENr321 119203171 chr8 ENr321 119224471 chr8 ENr321 119292071 chr8 ENm005 32721587 chr21 ENm005 32745887 chr21 ENm005 32786987 chr21 ENm005 32793487 chr21 ENm005 32991787 chr21 ENm005 33212187 chr21 ENm005 33675787 chr21 ENm005 33707887 chr21 ENm005 33950587 chr21 ENm005 33962587 chr21 ENm005 33978887 chr21 ENm005 33991787 chr21 ENm005 34065987 chr21 ENm005 34109887 chr21 ENm005 34118187 chr21 ENm005 34139087 chr21 ENm005 34188287 chr21 ENm005 34242387 chr21 ENm005 34262487 chr21 ENm005 34268987 chr21 ENm005 34317687 chr21 ENr311 53062426 chr14 ENr311 53073926 chr14 ENr311 53107626 chr14 ENr311 53116226 chr14 ENr311 53156126 chr14 ENr311 53173026 chr14 ENr311 53191626 chr14 ENr311 53416926 chr14 ENr111 29477666 chr13 ENr111 29494766 chr13 ENr111 29505966 chr13 ENr111 29585466 chr13 ENr111 29593366 chr13 ENr111 29599166 chr13 ENr111 29606566 chr13 ENr111 29615166 chr13 ENr111 29630266 chr13 ENr111 29644766 chr13 ENr111 29667166 chr13 ENr111 29812966 chr13 ENr111 29836766 chr13 ENr111 29861666 chr13 ENr111 29881566 chr13 ENr111 29903166 chr13 ENr231 148096784 chr1 ENr231 148157284 chr1 ENr231 148289184 chr1 ENr231 148298884 chr1 ENr231 148333984 chr1 ENr231 148367984 chr1 ENr231 148370384 chr1 ENr231 148382184 chr1 ENr231 148406184 chr1 ENm011 1798342 chr11 ENm011 1810642 chr11 ENm011 1822942 chr11 ENm011 1841742 chr11 ENm011 1854442 chr11 ENm011 1886142 chr11 ENm011 1933842 chr11 ENm011 1942542 chr11 ENm011 1948042 chr11 ENm011 1959342 chr11 ENm011 1967242 chr11 ENm011 1972042 chr11 ENm011 2013042 chr11 ENm011 2099142 chr11 ENm011 2281842 chr11 ENr333 33313079 chr20 ENr333 33357079 chr20 ENr333 33371379 chr20 ENr333 33378879 chr20 ENr333 33390279 chr20 ENr333 33484079 chr20 ENr333 33518579 chr20 ENr333 33612079 chr20 ENr333 33669579 chr20 ENr232 128968606 chr9 ENr232 128975206 chr9 ENr232 128983706 chr9 ENr232 128987206 chr9 ENr232 129007106 chr9 ENr232 129009406 chr9 ENr232 129026006 chr9 ENr232 129066706 chr9 ENr232 129078906 chr9 ENr232 129087506 chr9 ENr232 129164406 chr9 ENr232 129177206 chr9 ENr232 129192606 chr9 ENr232 129194306 chr9 ENr232 129244506 chr9 ENr232 129255706 chr9 ENm003 115977666 chr11 ENm003 116064166 chr11 ENm003 116072166 chr11 ENm003 116079166 chr11 ENm003 116203566 chr11 ENm003 116213566 chr11 ENm003 116228666 chr11 ENm003 116234366 chr11 ENm003 116250366 chr11 ENm003 116447766 chr11 ENm003 116449466 chr11 ENr332 63972839 chr11 ENr332 64090439 chr11 ENr332 64183739 chr11 ENr332 64200239 chr11 ENr332 64284139 chr11 ENr332 64367339 chr11 ENr332 64379239 chr11 ENr332 64387639 chr11 ENr332 64413139 chr11 ENr221 55889757 chr5 ENr221 55918057 chr5 ENr221 55939157 chr5 ENr221 55970257 chr5 ENr221 56019757 chr5 ENr221 56066257 chr5 ENr221 56094557 chr5 ENr221 56158157 chr5 ENr221 56168457 chr5 ENr221 56294457 chr5 ENm014 125923057 chr7 ENm014 125936157 chr7 ENm014 126038857 chr7 ENm014 126423357 chr7 ENm014 126443057 chr7 ENm001 115465022 chr7 ENm001 115505922 chr7 ENm001 115589622 chr7 ENm001 116016022 chr7 ENm001 116036322 chr7 ENm001 116104822 chr7 ENm001 116111122 chr7 ENm001 116392722 chr7 ENm001 116407622 chr7 ENm001 116485222 chr7 ENm001 116900622 chr7 ENm001 117062422 chr7 ENm001 117069922 chr7 ENm001 117101322 chr7 ENm001 117161922 chr7 ENm001 117216222 chr7 ENm001 117238322 chr7 ENm007 59186135 chr19 ENm007 59291535 chr19 ENm007 59369135 chr19 ENm007 59404535 chr19 ENr324 122658100 chrX ENr324 122674300 chrX