Table 2 Experimentally validated transcription factor binding sites.

Oct4

Ronin

R()†

Dejosez08

[89]

chr17

35643243

35643348

Oct4

Nr1b*/2b*; Rar*/Rxr*

HRE

Nordhoff01; Sylvester94

[59, 90]

chr17

35642936

35642955

+

Oct4

Nr6a1/GCNF

DR(0)

Fuhrmann01

[91]

chr17

35642943

35642955

+

Oct4

LRH1/Nr5a2

DR(0)

Gu05

[92]

chr17

35642943

35642955

+

Oct4

Nr2c1/TR2

DR(1)

Park07

[93]

chr17

35642936

35642949

+

Oct4

CoupTF1/Nr2f1

Schoorlemmer94

[94]

chr17

35642936

35642949

+

Oct4

CoupTF2/Nr2f2

Schoorlemmer94

[94]

chr17

35642936

35642949

+

Oct4

SF1

RARE

(a)

Barnea00

[95]

chr17

35642936

35642954

+

Oct4

Ear2/Nr2f6

Schoorlemmer94

[94]

chr17

35642936

35642949

+

Oct4

Sp1/3

Nordhoff01

[59]

chr17

35642929

35642939

+

Oct4

Zfp206

Yu09

[96]

chr17

35642877

35642886

+

Oct4

SF1

(b)

Barnea00

[95]

chr17

35642769

35642792

+

Oct4

Nobox

Choi06

[97]

chr17

35642612

35642618

+

Oct4

LRH1/Nr5a2

1B

PE2

Gu05

[92]

chr17

35642109

35642118

+

Oct4

Esrrb

P1

Zhang08

[66]

chr17

35642104

35642123

+

Oct4

Nanog

P1

Zhang08

[66]

chr17

35642033

35642054

+

Oct4

LRH1/Nr5a2

1B

PE1

Gu05

[92]

chr17

35642048

35642057

+

Oct4

Tcf3

M3

Tam08

[98]

chr17

35641942

35641948

+

Oct4

SF1

1A(PE)

Nordhoff01

[99]

chr17

35641863

35641873

+

Oct4

demethylation site

1A(PE)

Aoto06

[59, 99]

chr17

35641856

35641875

+

Oct4

Esrrb

P2

Zhang08

[66]

chr17

35641431

35641450

+

Oct4

Sall4

Zhang06

[100]

chr17

35641024

35641063

+

Oct4

OctSox

Chew05

[101]

chr17

35640993

35641008

+

Oct4

OctSox

2B

OkumuraN05

[102]

chr17

35640987

35641016

+

Oct4

Tcf3

M1

Tam08

[98]

chr17

35640793

35640799

+

Oct4

CR2

1B(PE)

Nordhoff01

[59]

chr17

35642037

35642063

Oct4

CR4

2A(DE)

Nordhoff01

[59]

chr17

35640947

35640965

Oct4

CR1

Nordhoff01

[59]

chr17

35642918

35643044

Oct4

CR2

Nordhoff01

[59]

chr17

35641981

35642181

Oct4

CR3

Nordhoff01

[59]

chr17

35641641

35641746

Oct4

CR4

Nordhoff01

[59]

chr17

35640937

35641068

Sox2

NF-Y

Wiebe00

[60]

chr3

34548868

34548886

+

Sox2

Lef1, Lef1

neural

Kamachi09

[48]

chr3

34564288

34564307

+

Sox2

FGF

neural

Kamachi09

[48]

chr3

34564324

34564330

+

Sox2

Oct4/6, Sox

Tomioka02

[82]

chr3

34552970

34552985

+

Sox2

Stat3

2

Foshay08

[103]

chr3

34548486

34548498

+

Sox2

Stat3

1

Foshay08

[103]

chr3

34545179

34545199

+

Sox2

Gli

1

Takanaga09

[104]

chr3

34545198

34545206

+

Sox2

Oct4; Brn1/2

1

Catena04

[105]

chr3

34545218

34545229

+

Sox2

Oct4; Brn1/2

2

Catena04

[105]

chr3

34545293

34545302

+

Sox2

HIF2alpha

HRE

1

MorenoM10

[106]

chr3

34547578

34547592

+

Sox2

HIF2alpha

HRE

2

MorenoM10

[106]

chr3

34548182

34548196

+

Sox2

Gli

2 dna_ not_matching^§

Takanaga09

[104]

chr3

34545074

34545085

Sox2

N1

neural

Kamachi09

[48]

chr3

34564105

34564403

Sox2

N2

neural

Kamachi09

[48]

chr3

34544940

34545478

Sox2

N3

neural

Kamachi09

[48]

chr3

34529134

34529728

Sox2

N4

neural

Kamachi09

[48]

chr3

34577673

34578140

Sox2

N5

neural

Kamachi09

[48]

chr3

34558702

34559054

Nanog

Oct1

Wu05

[107]

chr6

122657427

122657442

+

Nanog

OctSox

Rodda05; Kuroda05

[108, 69]

chr6

122657429

122657445

+

Nanog

Smad2/3/4

Greber10

[109]

chr6

122657408

122657412

+

Nanog

Klf4

R()†

Zhang10

[110]

chr6

122657370

122657550

Nanog

Stat

Suzuki06

[111]

chr6

122653091

122653100

+

Nanog

T

Suzuki06

[111]

chr6

122653135

122653155

+

Nanog

FoxD3

Pan06

[112]

chr6

122657311

122657341

+

Nanog

p53

RE1

Lin05

[113]

chr6

122656935

122656957

+

Nanog

p53

RE2

Lin05

[113]

chr6

122657195

122657221

+

Nanog

Klf

Jiang08

[114]

chr6

122652655

122652663

+

Nanog

Sp1/3

2

Wu06

[115]

chr6

122657555

122657570

+

Nanog

Sp1/3

1

Wu06

[115]

chr6

122657530

122657539

+

Nanog

Tcf3

Pereira06

[116]

chr6

122653837

122653844

+

Nanog

Gcnf/Nr6a1

Gu05

[92]

chr6

122655499

122655511

+

Nanog

Cdx2 and Nanog

R()†

Chen09

[117]

chr6

122652629

122652743

Nanog

Zfp143

revcom°

Chen08

[118]

chr6

122657340

122657354

+

Nanog

Esrrb

vdBerg08

[119]

chr6

122657409

122657418

+

Nanog

Klf5

Parisi08

[120]

chr6

122657532

122657539

+

Nanog

CR1

Chan09

[84]

chr6

122657170

122657827

Nanog

CR2

Chan09

[84]

chr6

122652641

122653468

Nanog

CR3

Chan09

[84]

chr6

122652431

122652696