Supplementary Table 1: ChIP-on-chip identified genes to which wild-type and mutant Htt are significantly bound to. Gene identifier and chromosomal location are in 7/7 the left two columns. Some genes are bound only by wild type Htt (STHdh ), some 111/111 exclusively by mutant Htt (STHdh ). A few genes are bound in both cell lines. Gene Chromosome Bound in 7/7 Bound in 111/111 Bound in both 0610006K04Rik chr19 7/7 0610027B03Rik-Kif18a chr2 7/7 0610030I09Rik chr2 111/111 0610040B21Rik chr4 7/7 0710001E13Rik chr9 111/111 1110030J09Rik chr11 7/7 1110031B11Rik chr3 7/7 1110032A13RikTxnl4 chr18 7/7 1110058L19Rik chr1 7/7 1110060O18Rik chr1 7/7 1500011L16Rik chr4 111/111 1600012F09Rik chr13 7/7 1600015H20Rik chr2 111/111 1700001L23Rik chr9 7/7 1700007K09Rik-1700063I17Rik chr7 7/7 1700014P03Rik chr7 111/111 1700020L24Rik chr11 111/111 1700026D08Rik chr7 7/7 111/111 Both 1700034E13Rik chr18 111/111 1700063I17Rik chr7 7/7 1700108M19Rik chr12 7/7 1700111I05Rik chr5 7/7 1810020G14Rik chr12 111/111 1810046J19RikGrb7 chr11 111/111 2010106E10Rik chrX 111/111 2310002B14Rik chr16 7/7 2310009E04Rik chr4 7/7 2310016A09Rik chr15 7/7 111/111 Both 2310016N21Rik chr5 7/7 2310034L04Rik chr17 111/111 2310042G06Rik chr2 111/111 2310045A20Rik chr5 111/111 2310057J18Rik chr10 7/7 2410004A20Rik chr9 7/7 2410042D21Rik chr2 111/111 2410116I05Rik chr4 7/7 2600005O03Rik chr15 7/7 2610014F08Rik chr2 7/7 2610027C15Rik chr4 7/7 2610209N15Rik chr11 7/7 111/111 Both 2610524H06Rik chr5 111/111 2610528M18RikMut chr17 111/111 2700029E10Rik chr14 7/7 2810052M02Rik chr3 7/7 2900016D05Rik chr17 7/7 111/111 Both 3110003A22Rik chr4 111/111 3110023G01Rik chr18 7/7 3930401K13Rik chr16 111/111 4122402O22Rik chr16 7/7 4632422M10Rik chr13 111/111 4831428F09 chr1 7/7 4921504I05Rik chr13 7/7 4921531G14Rik chr15 7/7 4930429A22Rik chr1 111/111 4930444A02Rik chr8 111/111 4930451A13Rik chr16 7/7 4930479M11Rik chr7 7/7 4930486G11Rik chr9 111/111 4930511H01Rik chr1 7/7 4930519N16Rik chr13 7/7 4930522D07Rik chr3 7/7 4930524B15Rik chr11 111/111 4931406I20Rik chr4 7/7 4931406P16Rik chr7 111/111 4931417A20 chr2 111/111 4933409D10Rik chr18 7/7 4933409K07Rik chr4 7/7 111/111 Both 4933417K05Rik chr10 111/111 5330410G16Rik chr8 7/7 6030441H18Rik chr7 111/111 6820429M01 chr7 7/7 9230106L14Rik chr2 7/7 111/111 Both 9430059P22Rik chr14 7/7 9530068E07Rik chr11 111/111 9530090G24Rik chr2 111/111 A630042L21Rik chr18 111/111 A730008L03Rik chr2 7/7 111/111 Both A730017C20Rik chr18 111/111 A830020B06Rik chr1 111/111 A830053O21Rik chr11 7/7 Aadac chr3 7/7 Abca8b chr11 7/7 Abcb11 chr2 7/7 Abcb1a chr5 111/111 Abcc6-Nomo1 chr7 111/111 Acoxl chr2 7/7 Acvrinp1 chr5 111/111 Adam24 chr8 7/7 Adam32 chr8 7/7 Adm chr7 7/7 Adm2 chr15 111/111 AdmrRdh1 chr10 7/7 Agtpbp1 chr13 7/7 Ahi1 chr10 111/111 Ahrr chr13 7/7 Akt1AI132321 chr12 7/7 Aldrl6 chr15 7/7 Alpk3 chr7 111/111 Als2cr3 chr1 7/7 Ambn chr5 111/111 Anapc7 chr5 7/7 Ankrd32 chr13 111/111 Aoc2 chr11 7/7 Apg10l chr13 7/7 Aplp2 chr9 111/111 Arhgap18 chr10 7/7 111/111 Both Armc8Dbr1 chr9 111/111 Arpc1b chr5 111/111 Art5 chr7 7/7 Asahl chr5 111/111 Asb14 chr14 111/111 Asb8 chr15 7/7 Ascl1 chr10 7/7 Asgr2 chr11 7/7 Atp2c1 chr9 7/7 Atrx chrX 7/7 AU018778 chr8 7/7 AW210596 chr19 111/111 B230358A15Rik chrX 7/7 B230399E16Rik chr18 111/111 B3galt5 chr16 111/111 Baat chr4 111/111 Bag2 chr1 7/7 BC018371 chr11 7/7 BC019561 chr18 7/7 BC020188 chr9 7/7 111/111 Both BC021785 chr10 111/111 BC026439 chr15 7/7 BC027057 chr13 7/7 BC032265 chr11 7/7 BC034097 chr11 7/7 111/111 Both BC037674 chr14 7/7 BC066107 chr17 7/7 Bex2 chrX 111/111 Bhlhb9 chrX 111/111 Bicd2 chr13 7/7 111/111 Both Bmpr1b chr3 7/7 Bok chr1 7/7 Brunol4 chr18 111/111 Btc chr5 7/7 Btg3 chr16 7/7 Btg4 chr9 7/7 C130057D23Rik chr4 7/7 C130068O12Rik chr15 7/7 111/111 Both C1ql1 chr11 7/7 C2 chr17 7/7 C230012O17Rik-Gpr63 chr4 7/7 C730014E05Rik chr16 111/111 Cacna1b chr2 7/7 Capn3 chr2 7/7 Caskin2 chr11 7/7 Ccnb1 chr13 7/7 Cd200r3 chr16 7/7 Cd52-D4Bwg1540e chr4 7/7 Cd99l2 chrX 111/111 Cdc91l1 chr2 7/7 Cdh11 chr8 111/111 Cdon chr9 7/7 Centd2 chr7 111/111 Chchd1 chr14 7/7 Chic1 chrX 7/7 chr1:161739566-161739626 chr1 111/111 chr12:109234647109234707 chr12 111/111 chr14:5657693956576999 chr14 111/111 chr16:4283083142830771 chr16 111/111 chr16:7800562678005686 chr16 111/111 chr16:8958744789587507 chr16 7/7 111/111 Both chr17:8460947984609539 chr17 111/111 chrY:15027747-15027687 chrY 7/7 111/111 Both chrY:15027967-15028027 chrY 111/111 chrY:15028307-15028247 chrY 111/111 chrY:15028475-15028535 chrY 7/7 111/111 Both chrY:17146080-17146140 chrY 7/7 111/111 Both chrY:34924552-34924492 chrY 7/7 111/111 Both chrY:3649958-3649898 chrY 111/111 chrY:3650178-3650238 chrY 111/111 chrY:39819170-39819110 chrY 111/111 chrY:41073447-41073387 chrY 7/7 111/111 Both chrY:5814034-5813974 chrY 111/111 Chuk chr19 7/7 Cidec-Jagn1 chr6 111/111 Clca2 chr3 7/7 Clec4a2 chr6 7/7 Clec4d chr6 7/7 111/111 Both Clec9a chr6 7/7 Clu chr14 7/7 Cml1 chr6 111/111 Cntf chr19 7/7 111/111 Both Cpa1 chr6 7/7 Cpa5 chr6 7/7 Cpeb3 chr19 111/111 Cpeb4 chr11 7/7 Crat-Ppp2r4 chr2 111/111 Crbn chr6 7/7 Crisp3 chr17 7/7 Csna chr5 111/111 Csnk chr5 111/111 Cspg5 chr9 7/7 Ctla4 chr1 7/7 Ctps2 chrX 7/7 Cyct-Drbp1 chr2 111/111 Cyp2c29 chr19 7/7 Cyp2c55 chr19 111/111 Cyp2d13 chr15 111/111 Cyp2e1 chr7 7/7 Cyp2j9 chr4 7/7 D10Ertd214eIpmk chr10 111/111 D10Wsu52e chr10 111/111 D12Ertd553e chr12 7/7 D17Ertd288e chr17 7/7 D230005D02Rik chr14 7/7 D330012D11Rik chr11 7/7 111/111 Both D430020F16 chr7 7/7 D4Ertd22e-Fbxo42 chr4 111/111 D630003K02Rik chr7 111/111 D730040F13Rik chr4 7/7 D830007F02Rik chr8 7/7 111/111 Both Dad1Abhd4 chr14 111/111 Ddx26 chr14 111/111 Ddx3y chrY 111/111 Defb14 chr8 111/111 Defb39 chr8 7/7 Dek chr13 7/7 Dnajc2 chr5 111/111 Dncl2b chr8 7/7 Doc2a chr7 7/7 Dpp10 chr1 7/7 111/111 Both Dsg3 chr18 7/7 Dtna chr18 7/7 Dusp13 chr14 111/111 E030025L21Rik chr12 7/7 E130114P18Rik chr4 111/111 Eapa2 chr6 7/7 Eef1a2 chr2 7/7 Elac2 chr11 111/111 Elovl2 chr13 111/111 Elovl3 chr19 7/7 Elovl4 chr9 7/7 Emr1 chr17 7/7 Enam chr5 7/7 Enpp3 chr10 7/7 Ep400 chr5 111/111 Epb4.1l3 chr17 7/7 111/111 Both Epc1 chr18 7/7 Ephx2 chr14 111/111 Epn3 chr11 7/7 Eral1 chr11 111/111 Esco22610528H13Rik chr14 7/7 Evc-Evc2 chr5 111/111 F13a1 chr13 111/111 Fabp7 chr10 111/111 Fbl chr7 7/7 Fbn1 chr2 7/7 111/111 Both Fbxw15 chr9 7/7 Fgb chr3 111/111 Fgf12 chr16 111/111 Fgl2 chr5 7/7 Fkrp chr7 111/111 Fntb chr12 111/111 Foxf1a chr8 111/111 Foxm1 chr6 7/7 Frat1 chr19 7/7 Fshb chr2 111/111 Fshprh1 chrX 7/7 Fv1 chr12 7/7 Gad1 chr2 7/7 Galnt6 chr15 7/7 Gata6 chr18 111/111 Gbp5 chr3 7/7 Gc chr5 7/7 Gcap14 chr14 111/111 Gcgr chr11 7/7 Gchfr chr2 111/111 Gif chr19 111/111 Gjb6 chr14 7/7 Glt25d1 chr8 111/111 Gmfg chr7 7/7 Gnpda2 chr5 7/7 Gpa33 chr1 7/7 Gpm6a chr8 111/111 Gpr128 chr16 111/111 Gpr40 chr7 7/7 111/111 Both Gspt1 chr16 111/111 Gstz1 chr12 7/7 111/111 Both Guca1b chr17 111/111 Gys2 chr6 111/111 Gzmb chr14 111/111 H2 chr17 7/7 H28 chr3 7/7 Hace1 chr10 7/7 Hdhd1a chr18 111/111 Helz chr11 7/7 Hivep1 chr13 7/7 Hlx1 chr1 7/7 111/111 Both Hmmr chr11 7/7 HnrpcRpgrip1 chr14 7/7 Hps6 chr19 7/7 Hrh4 chr18 111/111 Hrpt2 chr1 111/111 Hsd3b1 chr3 7/7 Hspa12a chr19 111/111 Hspb3 chr13 111/111 Hyal3 chr9 111/111 Ibsp chr5 111/111 Ifitm2-Ifitm1 chr7 7/7 Ifna5 chr4 7/7 Ighg chr12 7/7 111/111 Both Il17f chr1 7/7 Il1f5 chr2 111/111 Ipo4 chr14 111/111 Isyna1 chr8 111/111 Itgae chr11 7/7 Itgb3bp chr4 7/7 111/111 Both Jam3 chr9 111/111 Jarid1b chr1 111/111 Junb chr8 7/7 Kbtbd4 chr2 7/7 Kcna7 chr7 7/7 Kcnab2 chr4 7/7 Kera chr10 7/7 111/111 Both Kif22 chr7 111/111 Kif2a chr13 111/111 Klk4 chr7 7/7 Klrc2 chr6 7/7 111/111 Both Klrc3 chr6 111/111 Klrk1 chr6 7/7 111/111 Both Krtap16 chr16 111/111 Krtap21 chr16 111/111 Lancl3 chrX 111/111 Lao1 chr4 7/7 111/111 Both Lass1 chr8 111/111 Liph chr16 7/7 Lipl2 chr19 7/7 Lmo2 chr2 7/7 LOC382133 chrY 7/7 LOC432534 chr11 7/7 111/111 Both LOC433332 chr1 7/7 Lrrc21 chr14 7/7 Lrrc5 chr5 7/7 Ltbp1 chr17 111/111 Lum chr10 7/7 Mad chr6 111/111 Mad2l1bp chr17 111/111 Mag chr7 7/7 Magoh chr4 111/111 Man2b1 chr8 7/7 Mapk8 chr14 111/111 Matn2 chr15 7/7 Mb chr15 7/7 Mbl1 chr14 7/7 Meig1-Dclre1c chr2 7/7 Meox2 chr12 7/7 Mfap4 chr11 7/7 MGC54654 chr15 7/7 Mgea6 chr12 7/7 Mgst1 chr6 111/111 Mib1 chr18 7/7 111/111 Both Mid1 chrX 7/7 Mmp10 chr9 7/7 Mmp1a chr9 7/7 111/111 Both Mobkl2b chr4 7/7 Mobkl2c chr4 7/7 111/111 Both Mog chr17 7/7 MOR118 chr14 7/7 Morc chr16 7/7 Mpl chr4 7/7 Mpp5 chr12 7/7 Mrgprb4 chr7 111/111 Mrpl16 chr19 7/7 Mrpl27 chr11 7/7 111/111 Both Ms4a7 chr19 7/7 Mtpn chr6 111/111 Muc10 chr5 7/7 111/111 Both Mup4 chr4 111/111 Mustn1 chr14 111/111 Mybpc3 chr2 7/7 Myl2 chr5 111/111 Myo1g chr11 7/7 Myo7a chr7 7/7 111/111 Both Naca chr10 7/7 Nalp4b chr7 111/111 Nalp5 chr7 7/7 Narg1lMtrf1 chr14 7/7 Ndufs6Mrpl36 chr13 7/7 Nedd8 chr14 111/111 Neto1 chr18 7/7 111/111 Both Neurod2 chr11 7/7 Nf1 chr11 7/7 111/111 Both Nkx1 chr7 111/111 Nol6 chr4 111/111 Nola2 chr11 7/7 Notch1 chr2 7/7 Npr1-Ilf2 chr3 7/7 Nr1d1 chr11 7/7 Nr1i2Popdc2 chr16 111/111 Nrbp chr5 7/7 Nrip3 chr7 111/111 Nsf chr11 111/111 Nudt1 chr5 111/111 Nudt7 chr8 111/111 Nxf2 chrX 7/7 Olfr1036 chr2 111/111 Olfr108 chr17 111/111 Olfr1094 chr2 111/111 Olfr11 chr13 7/7 111/111 Both Olfr1123 chr2 7/7 111/111 Both Olfr1138-Olfr1140 chr2 111/111 Olfr1176 chr2 7/7 Olfr1183 chr2 7/7 111/111 Both Olfr1184 chr2 111/111 Olfr129 chr17 111/111 Olfr1324 chrX 7/7 Olfr134 chr17 111/111 Olfr1370 chr13 7/7 Olfr139 chr11 111/111 Olfr1406 chr1 7/7 Olfr1426 chr19 7/7 Olfr1433 chr19 7/7 Olfr1440 chr19 7/7 Olfr1457 chr19 7/7 Olfr1509 chr14 111/111 Olfr1510 chr14 7/7 Olfr164 chr16 7/7 Olfr166 chr16 111/111 Olfr168 chr16 7/7 Olfr181 chr16 111/111 Olfr187 chr16