Table S2. Sequences immunoprecipitating with anti-hif-1α

Genome-wide analysis of HIF DNA-bdg-supplemental material Table S2. Sequences immunoprecipitatg with anti-α The table gives the chromosomal co-ordates of each anti-α immunoprecipitated locus meetg criteria of an MA Z of > 4, a width of > 100bp or > 5 probes, and a false discovery rate of < 5%, together with the maximum Z anti-α and anti-α at that gene locus. The presence or absence, and position of any HRE core motif with these sequences is given. The table also specifies whether the nearest gene to the immunoprecipitated locus was significantly regulated by exposure of cells to 1% hypoxia or 2mM DMOG or by transfection of sirnas directed agast α, α or both sirnas the Affymetrix s. Note that at a of loci several sequences were immunoprecipitated that shared proximity to a common transcriptional start site. These loci are listed order with the most strongly enriched site dicated black type and others grey type. Name chromosome start end Strand Coordates of 1 ASMT ACETYLSEROTONIN O-METHYLTRANSFERASE NM_004043 No chrx 1842483 1844214 + 17.9 21.9 Yes 1844025, 1844146 2 PLS3 PLASTIN 3 (T ISOFORM) NM_005032 No chrx 114898432 114899202 + 15.8 17.4 Yes 114898465, 114898462, 114898505, 114898572, 114898984, 114899078, 114899133, 114899130 3 GPI GLUCOSE PHOSPHATE ISOMERASE NM_000175 No chr19 39541340 39542126 + 15.7 9.6 Yes 39542049, 39542060, 39542057, 39542073, 39542083 chr19 39540468 39540783 + 7.4 No 4 DARS ASPARTYL-TRNA SYNTHETASE NM_001349 Yes chr2 136458510 136459327-15.5 9.8 Yes 136458864, 136458861, 136459117, 136459126, 136459217, 136459320 5 SNAPC1 SMALL NUCLEAR RNA ACTIVATING COMPLEX, POLYPEPTIDE NM_003082 No chr14 61291513 61291955 + 13.9 6.0 No 1, 43KDA 6 SEC61G SEC61 GAMMA SUBUNIT NM_001012456 No chr7 54794557 54794993-13.4 12.2 Yes 54794651 7 GTF2IRD2B GTF2I REPEAT DOMAIN CONTAINING 2B NM_001003795 No chr7 74146820 74147110 + 12.7 7.1 No chr7 74145407 74145716 + 6.1 No chr7 74147633 74147933 + 5.4 No 8 SAP30 SIN3A-ASSOCIATED PROTEIN, 30KDA NM_003864 Yes chr4 174527153 174528353 + 12.6 9.3 Yes 174527527, 174527558, 174527857 9 ZMYND8 PROTEIN KINASE C BINDING PROTEIN 1 NM_012408 Yes chr20 45422559 45423749-12.1 15.2 Yes 45422676 chr20 45421122 45421975-9.3 Yes 45421140, 45421318 chr20 45416738 45416961-5.4 No chr20 45324234 45324808-5.3 Yes 45324630 chr20 45382266 45382561-5.2 No chr20 45381728 45381912-5.0 No chr20 45322893 45323036-4.8 No chr20 45380596 45380865-4.7 No 10 RSBN1 ROUND SPERMATID BASIC PROTEIN 1 NM_018364 Yes chr1 114156633 114157374-11.9 6.0 Yes 114156709, 114156726, 114157241 chr1 114154609 114155069-5.4 Yes 114154800 chr1 114154093 114154264-5.1 No 11 BNIP3L BCL2/ADENOVIRUS E1B 19KDA INTERACTING PROTEIN 3-LIKE NM_004331 Yes chr8 26297111 26297957 + 11.9 7.9 Yes 26297111, 26297203, 26297250, 26297247, 26297409 12 FAM139A HYPOTHETICAL PROTEIN FLJ40722 NM_173678 Yes chr7 143028228 143029042 + 11.8 14.0 Yes 143028431, Supplemental material Page 2

Genome-wide analysis of HIF DNA-bdg-supplemental material Name chromosome start end Strand Coordates of 143028490 13 GTF2IRD2 GTF2I REPEAT DOMAIN CONTAINING 2 NM_173537 No chr7 73904992 73905289-11.6 Yes 73905205 chr7 73906359 73906641-6.5 No 14 C3ORF28 CHROMSOME 3 OPEN READING FRAME 28 NM_014367 Yes chr3 123584923 123585595 + 11.6 4.9 No chr3 123586518 123586736 + 4.7 No chr3 123585892 123586061 + 4.6 No 15 STC2 STANNIOCALCIN 2 NM_003714 Yes chr5 172688209 172689013-11.2 8.8 Yes 172688835 chr5 172689765 172690086-6.0 Yes 172689880 16 NARF NUCLEAR PRELAMIN A RECOGNITION FACTOR NM_001038618 Yes chr17 78008958 78009355 + 10.9 No 17 TF TRANSFERRIN NM_001063 No chr3 134944094 134944856 + 10.7 13.6 Yes 134944391 18 HK2 HEXOKINASE 2 NM_000189 Yes chr2 74914233 74914441 + 10.5 5.6 Yes 74914327, 74914395 chr2 74912970 74913723 + 6.9 No 19 INHA INHIBIN, ALPHA NM_002191 Yes chr2 220149206 220150032 + 10.4 9.1 Yes 220150014, 220150031 chr2 220150797 220151070 + 5.2 No 20 PCF11 KIAA0824 PROTEIN NM_015885 No chr11 82544764 82545226 + 10.3 8.1 Yes 82544944, 82544960, 82545204 21 C9ORF30 CHROMOSOME 9 OPEN READING FRAME 30 NM_080655 No chr9 102228622 102228900 + 10.3 9.7 Yes 102228764, 102228847 chr9 102231225 102231536 + 5.9 Yes 102231461 22 CBWD3 COBW DOMAIN CONTAINING 3 NM_201453 No chr9 70046581 70047378 + 10.2 5.1 Yes 70046687, 70046696, 70046716, 70046750, 70047185, 70047347, 70047344 23 RAD51L1 RAD51-LIKE 1 (S. CEREVISIAE) NM_133510 Yes chr14 67356360 67357875 + 9.8 8.2 Yes 67356452, 67356989, 67357024, 67357176 24 KIAA0195 KIAA0195 NM_014738 No chr17 70960840 70961202 + 9.7 11.6 Yes 70960909 25 S100P S100 CALCIUM BINDING PROTEIN P NM_005980 Yes chr4 6721070 6721680 + 9.7 9.4 Yes 6721099 26 CDKN1B CYCLIN-DEPENDENT KINASE INHIBITOR 1B (P27, KIP1) NM_004064 No chr12 12769409 12771043 + 9.6 7.2 Yes 12769932, 12770596 chr12 12767627 12767812 + 4.5 No 27 NFE2L1 NUCLEAR FACTOR (ERYTHROID-DERIVED 2)-LIKE 1 NM_003204 No chr17 43481265 43481686 + 9.6 7.5 Yes 43481343, 43481611 28 HIG2 HYPOXIA-INDUCIBLE PROTEIN 2 NM_013332 Yes chr7 127882554 127883158 + 9.5 12.1 Yes 127882971, 127883052, 127883064, 127883083, 127883101, 127883122 29 QSOX1 QUIESCIN Q6 NM_002826 Yes chr1 178403034 178403880 + 9.5 4.7 No 30 INSIG2 INSULIN INDUCED GENE 2 NM_016133 Yes chr2 118561723 118562366 + 9.5 9.0 Yes 118562210, 118562237, 118562361 chr2 118559287 118560379 + 7.0 No chr2 118561033 118561352 + 5.9 Yes 118561303 31 ARRDC3 ARRESTIN DOMAIN CONTAINING 3 NM_020801 No chr5 90612425 90613294-9.4 10.6 Yes 90612574, 90612633, 90613180 32 ALKBH5 ALKB, ALKYLATION REPAIR HOMOLOG 5 (E. COLI) NM_017758 No chr17 18026917 18027548 + 9.3 4.9 Yes 18027105, 18027425 chr17 18026334 18026583 + 7.4 No 33 FLJ16641 FLJ16641 PROTEIN NM_001004316 No chr3 158017688 158018251 + 9.3 10.8 Yes 158017699, 158017762, 158018158 chr3 158027241 158027560 + 8.6 Yes 158027322, 158027361, 158027379, 158027421, 158027489, 158027538 chr3 158012869 158013189 + 6.9 Yes 158013112 34 MAX MYC ASSOCIATED FACTOR X NM_145114 No chr14 64763248 64764004-9.2 5.1 Yes 64763593 35 ZNF398 ZINC FINGER PROTEIN 398 NM_020781 No chr7 148455184 148455391 + 9.1 Yes 148455348 36 PAICS PHOSPHORIBOSYLAMINOIMIDAZOLE CARBOXYLASE, PHOSPHORIBOSYLAMINOIMIDAZOLE SUCCINOCARBOXAMIDE SYNTHETASE NM_006452 No chr4 56997994 56998436 + 9.1 7.3 No Supplemental material Page 3

Genome-wide analysis of HIF DNA-bdg-supplemental material Name chromosome start end Strand Coordates of 37 CBWD2 COBW DOMAIN CONTAINING 2 NM_172003 No chr2 113911827 113912527 + 9.0 Yes 113911835, 113911844, 113911864, 113911898, 113912096, 113912333, 113912495, 113912492 38 GNAI3 GUANINE NUCLEOTIDE BINDING PROTEIN (G PROTEIN), NM_006496 No chr1 109890497 109891164 + 8.9 4.5 Yes 109890631 ALPHA INHIBITING ACTIVITY POLYPEPTIDE 3 39 PPP1R3C PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) SUBUNIT 3C NM_005398 Yes chr10 93383091 93383567-8.9 6.4 No chr10 93382083 93382548-7.5 Yes 93382455 40 BBX BOBBY SOX HOMOLOG (DROSOPHILA) NM_020235 Yes chr3 108725637 108726237 + 8.9 Yes 108726060, 108726225 41 PNPLA8 INTRACELLULAR MEMBRANE-ASSOCIATED CALCIUM- INDEPENDENT PHOSPHOLIPASE A2 GAMMA 42 PFKFB3 6-PHOSPHOFRUCTO-2-KINASE/FRUCTOSE-2,6-BIPHOSPHATASE 3 NM_015723 No chr7 107954054 107954453-8.9 3.6 Yes 107954063, 107954081, 107954434 NM_004566 Yes chr10 6283565 6284210 + 8.8 4.7 Yes 6283611, 6283620, 6283913 chr10 6282266 6282711 + 5.9 No 43 C5ORF15 HYPOTHETICAL PROTEIN 23851 NM_020199 No chr5 133332337 133332780-8.7 5.2 Yes 133332392 44 BACE2 BETA-SITE APP-CLEAVING ENZYME 2 NM_138992 Yes chr21 41458829 41459988 + 8.7 11.4 Yes 41459310, 41459982 45 UPK1B UROPLAKIN 1B NM_006952 No chr3 120386306 120387020 + 8.6 11.7 Yes 120386572 46 FAM13A1 FAMILY WITH SEQUENCE SIMILARITY 13, MEMBER A1 NM_001015045 Yes chr4 89963666 89964441-8.5 8.1 Yes 89963987, 89964009 47 CCNG2 CYCLIN G2 NM_004354 Yes chr4 78298672 78299125 + 8.5 8.0 No 48 CYP27C1 FLJ16008 PROTEIN NM_001001665 No chr2 127700888 127701131-8.3 10.5 Yes 127700981 49 OXSM 3-OXOACYL-ACP SYNTHASE, MITOCHONDRIAL NM_017897 No chr3 25806215 25807745 + 8.2 5.7 Yes 25806428 50 CBWD5 COBW DOMAIN CONTAINING 5 NM_001024916 No chr9 69729281 69729934-8.1 Yes 69729310, 69729307, 69729469, 69729904 51 CITED2 CBP/P300-INTERACTING TRANSACTIVATOR, WITH GLU/ASP- RICH CARBOXY-TERMINAL DOMAIN, 2 NM_006079 Yes chr6 139738367 139739480-8.1 12.1 Yes 139738573, 139738619, 139738629, 139738646 52 C12ORF36 CHROMOSOME 12 OPEN READING FRAME 36 NM_182558 No chr12 13421413 13421589-8.1 6.6 Yes 13421528 53 RAPGEF6 RAP GUANINE NUCLEOTIDE EXCHANGE FACTOR (GEF) 6 NM_016340 No chr5 130998954 130999756-8.1 Yes 130999250 54 LOC401152 HCV F-TRANSACTIVATED PROTEIN 1 NM_001001701 Yes chr4 120440308 120441137-8.0 5.7 Yes 120440465, 120440755 chr4 120441498 120441681-6.6 Yes 120441555 chr4 120442948 120443179-4.5 No 55 JMJD1A JUMONJI DOMAIN CONTAINING 1A NM_018433 Yes chr2 86520791 86521639 + 7.9 6.2 Yes 86520948, 86521299, 86521358, 86521355, 86521477 56 TFRC TRANSFERRIN RECEPTOR (P90, CD71) NM_003234 No chr3 197293629 197294131-7.9 3.9 Yes 197293750 57 CRKL V-CRK SARCOMA VIRUS CT10 ONCOGENE HOMOLOG (AVIAN)-LIKE NM_005207 No chr22 19600989 19601171 + 7.7 7.3 No chr22 19602640 19602845 + 7.2 Yes 19602809 chr22 19603871 19604189 + 5.5 No 58 TRIM37 TRIPARTITE MOTIF-CONTAINING 37 NM_015294 No chr17 54539430 54539819-7.7 4.3 No chr17 54540425 54540603-4.5 No 59 FOXN3 CHECKPOINT SUPPRESSOR 1 NM_005197 No chr14 88951482 88952201-7.7 3.5 No 60 PIK3C2G PHOSPHOINOSITIDE-3-KINASE, CLASS 2, GAMMA POLYPEPTIDE NM_004570 No chr12 18305375 18305910 + 7.7 8.5 Yes 18305385, 18305636, 18305682 61 FOXO3 FORKHEAD BOX O3A NM_201559 No chr6 108986598 108987068 + 7.6 3.3 Yes 108986707, 62 SLC2A1 SOLUTE CARRIER FAMILY 2 (FACILITATED GLUCOSE TRANSPORTER), MEMBER 1 63 GBE1 GLUCAN (1,4-ALPHA-), BRANCHING ENZYME 1 (GLYCOGEN BRANCHING ENZYME, ANDERSEN DISEASE, GLYCOGEN STORAGE DISEASE TYPE IV) NM_006516 Yes chr1 43201121 43201658-7.6 6.7 No 108986834 NM_000158 Yes chr3 81892043 81893145-7.6 5.0 Yes 81892811, 81892808, 81892831, 81892849, 81892938 64 DTNA DYSTROBREVIN, ALPHA NM_001392 Yes chr18 30326823 30327364 + 7.5 5.6 Yes 30327015, 30327012, 30327112 Supplemental material Page 4

Genome-wide analysis of HIF DNA-bdg-supplemental material Name chromosome start end Strand Coordates of 65 CHD1L CHROMODOMAIN HELICASE DNA BINDING PROTEIN 1-LIKE NM_004284 No chr1 145181448 145181775 + 7.5 11.9 Yes 145181605, 145181698, 145181738 66 CARD14 CASPASE RECRUITMENT DOMAIN FAMILY, MEMBER 14 NM_024110 No chr17 75754905 75755466 + 7.5 No 67 UBC UBIQUITIN C NM_021009 No chr12 123966840 123967854-7.4 11.2 No chr12 123968105 123968404-5.4 No chr12 123989881 123990287-5.0 No 68 IVNS1ABP INFLUENZA VIRUS NS1A BINDING PROTEIN NM_006469 No chr1 183553518 183554274-7.4 6.2 Yes 183553574, 183553769, 183553957, 183554009, 183554006 69 ILVBL ILVB (BACTERIAL ACETOLACTATE SYNTHASE)-LIKE NM_006844 Yes chr19 15101831 15102474-7.4 7.8 Yes 15102202 70 CBWD1 COBW DOMAIN CONTAINING 1 NM_018491 No chr9 168601 168994-7.3 3.2 Yes 168787, 168985 71 LDHA LACTATE DEHYDROGENASE A NM_005566 No chr11 18372041 18372531 + 7.2 3.6 Yes 18372504, 18372501 72 FAM110C TRANSFERRIN NM_001077710 No chr2 37063 37485-7.2 6.0 Yes 37109, 37447 73 BAMBI BMP AND ACTIVIN MEMBRANE-BOUND INHIBITOR HOMOLOG (XENOPUS LAEVIS) NM_012342 No chr10 29232284 29232905 + 7.2 8.3 Yes 29232772, 29232771, 29232775 74 IARS2 ISOLEUCINE-TRNA SYNTHETASE 2, MITOCHONDRIAL NM_018060 No chr1 218334563 218334781 + 7.1 2.7 Yes 218334719 75 DYNLL1 DYNEIN, LIGHT CHAIN, LC8-TYPE 1 NM_001037494 No chr12 119396899 119397976 + 7.1 6.6 Yes 119397037 76 RASEF RAS AND EF-HAND DOMAIN CONTAINING NM_152573 No chr9 84868094 84868488-7.1 5.1 Yes 84868110 77 IQCG HYPOTHETICAL PROTEIN FLJ23571 NM_032263 No chr3 199170897 199171248-7.1 3.3 No 78 HIST2H3PS2 HISTONE 1, H2BD NM_021063 Yes chr6 26267512 26268031 + 7.1 4.1 Yes 26267555, 26267822, 26268005 79 MTP18 MITOCHONDRIAL PROTEIN 18 KDA NM_016498 No chr22 29150748 29151030 + 7.0 4.8 No chr22 29149767 29149951 + 4.2 Yes 29149931 80 SFRS18 CHROMOSOME 6 OPEN READING FRAME 111 NM_032870 No chr6 99979989 99981157-7.0 4.4 Yes 99979997, 99979994, 99980093, 99980203, 99980479, 99980926 81 HSPA9 HEAT SHOCK 70KDA PROTEIN 9B (MORTALIN-2) NM_004134 No chr5 137939562 137939722-7.0 3.7 No 82 HIST2H4B H4 HISTONE, FAMILY 2 NM_003548 Yes chr1 148072856 148073094 + 7.0 3.1 No chr1 148068515 148069844 + 5.7 No chr1 148100602 148101493 + 5.2 No 83 CDC73 CELL DIVISION CYCLE 73, PAF1/RNA POLYMERASE II NM_024529 No chr1 191356703 191357153 + 7.0 3.3 No COMPLEX COMPONENT, HOMOLOG (S. CEREVISIAE) 84 CARHSP1 SMALL NUCLEAR RNA ACTIVATING COMPLEX, POLYPEPTIDE NM_001042476 No chr16 8869189 8869514-7.0 5.1 Yes 8869404 3, 50KDA 85 USP32 UBIQUITIN SPECIFIC PEPTIDASE 32 NM_032582 No chr17 55824707 55825054-6.9 2.4 No chr17 55823201 55823517-4.7 No 86 TRIM16 TRIPARTITE MOTIF-CONTAINING 16 NM_006470 No chr17 15489887 15490230-6.9 9.2 Yes 15489888 87 C1ORF192 CHROMOSOME 1 OPEN READING FRAME 192 NM_001013625 No chr1 159664439 159665066-6.9 4.2 Yes 159664655 88 MS4A7 MEMBRANE-SPANNING 4-DOMAINS, SUBFAMILY A, MEMBER NM_021201 No chr11 59895048 59895265 + 6.9 8.5 No 7 89 DDB2 DAMAGE-SPECIFIC DNA BINDING PROTEIN 2, 48KDA NM_000107 No chr11 47193563 47194079 + 6.9 3.6 Yes 47193719, 47193734 90 FBXO42 F-BOX PROTEIN 42 NM_018994 No chr1 16551857 16552191-6.9 6.0 No chr1 16550206 16550522-5.1 No 91 C1ORF161 CHROMOSOME 1 OPEN READING FRAME 161 NM_152367 No chr1 116455368 116456717 + 6.9 11.2 Yes 116455489, 116455851 chr1 116453958 116454531 + 5.4 No 92 TMEM97 TRANSMEMBRANE PROTEIN 97 NM_014573 No chr17 23677321 23677743 + 6.9 6.6 Yes 23677520 93 SNAPC3 SMALL NUCLEAR RNA ACTIVATING COMPLEX, POLYPEPTIDE 3, 50KDA NM_001039697 No chr9 15412123 15412387 + 6.8 5.1 Yes 15412314, 15412354 94 TMEM48 TRANSMEMBRANE PROTEIN 48 NM_018087 No chr1 54075898 54076186-6.7 2.4 No 95 SCYL1 SCY1-LIKE 1 (S. CEREVISIAE) NM_020680 No chr11 65031173 65031480 + 6.7 5.5 Yes 65031247, 65031424 chr11 65022543 65022868 + 5.1 Yes 65022570 96 CGA GLYCOPROTEIN HORMONES, ALPHA POLYPEPTIDE NM_000735 No chr6 87922808 87923255-6.7 2.8 No chr6 87921131 87921454-5.6 Yes 87921418 97 TMEM107 TRANSMEMBRANE PROTEIN 107 NM_183065 Yes chr17 8017992 8018283-6.7 4.0 No 98 PDLIM2 PDZ-LIM PROTEIN MYSTIQUE NM_001013842 Yes chr8 22511328 22511635 + 6.7 9.3 No 99 SMG1 PI-3-KINASE-RELATED KINASE SMG-1 NM_015092 No chr16 18846597 18846919-6.7 3.3 Yes 18846629, 18846679, 18846696 100 DNASE1 DEOXYRIBONUCLEASE I NM_005223 Yes chr16 3636514 3637238 + 6.7 5.0 Yes 3636615, 3636819 Supplemental material Page 5

Genome-wide analysis of HIF DNA-bdg-supplemental material Name Supplemental material Page 6 chromosome start end Strand Coordates of 3636819 101 DHRS13 HYPOTHETICAL PROTEIN MGC23280 NM_144683 Yes chr17 24254500 24254750-6.7 3.5 Yes 24254517, 24254716, 24254713 102 TEX14 TESTIS EXPRESSED SEQUENCE 14 NM_031272 No chr17 54118808 54119196-6.7 5.6 No 103 HIST1H1C HISTONE 1, H1C NM_005319 No chr6 26163162 26163550-6.7 7.2 Yes 26163390 104 SOSTDC1 SCLEROSTIN DOMAIN CONTAINING 1 NM_015464 No chr7 16426189 16426730-6.7 4.7 Yes 16426227, 16426249 105 RBPJ RECOMBINING BINDING PROTEIN SUPPRESSOR OF HAIRLESS NM_203283 Yes chr4 25929762 25929951 + 6.6 4.1 Yes 25929896 (DROSOPHILA) 106 C11ORF30 CHROMOSOME 11 OPEN READING FRAME 30 NM_020193 No chr11 75832552 75833346 + 6.6 3.3 Yes 75832646, 75832973, 75833057, 75833054, 75833170 107 POM121 POM121 MEMBRANE GLYCOPROTEIN (RAT) NM_172020 No chr7 71987404 71987627 + 6.6 4.9 No chr7 71988592 71988736 + 4.4 No 108 IER3 IMMEDIATE EARLY RESPONSE 3 NM_003897 No chr6 30827231 30827777-6.6 7.8 No 109 CP CERULOPLASMIN (FERROXIDASE) NM_000096 No chr3 150425412 150425864-6.6 7.3 Yes 150425807 110 RNF183 RING FINGER PROTEIN 183 NM_145051 Yes chr9 115105187 115105643-6.5 3.4 Yes 115105206, 115105249 111 PNRC1 PROLINE-RICH NUCLEAR RECEPTOR COACTIVATOR 1 NM_006813 Yes chr6 89848399 89848986 + 6.5 No 112 C8ORF44 CHROMOSOME 8 OPEN READING FRAME 44 NM_019607 No chr8 67749275 67749461 + 6.5 4.9 No 113 BCL2L2 BCL2-LIKE 2 NM_004050 No chr14 22839864 22840201 + 6.5 3.1 No 114 TTLL2 TUBULIN TYROSINE LIGASE-LIKE FAMILY, MEMBER 2 NM_031949 No chr6 167653391 167653677 + 6.5 8.4 Yes 167653443, 167653457 115 FLJ10292 MAGO-NASHI HOMOLOG NM_018048 No chr12 10657648 10658011-6.5 No 116 PDE4DIP PHOSPHODIESTERASE 4D INTERACTING PROTEIN NM_001002811 No chr1 143644097 143644426-6.5 4.2 No (MYOMEGALIN) chr1 143792312 143792485-4.0 No 117 SMC2 SMALL NUCLEAR RNA ACTIVATING COMPLEX, POLYPEPTIDE 3, 50KDA NM_001042550 No chr9 105896290 105897168 + 6.5 3.4 Yes 105896584, 105896590 118 PPP1R15B PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) NM_032833 No chr1 202652958 202653489-6.4 7.1 No SUBUNIT 15B 119 C6ORF170 CHROMOSOME 6 OPEN READING FRAME 170 NM_152730 No chr6 121697689 121697975-6.4 2.9 No 120 LOC642980 SMALL NUCLEAR RNA ACTIVATING COMPLEX, POLYPEPTIDE NM_001039761 No chrx 148436030 148436391 + 6.4 5.9 No 3, 50KDA 121 HLA-G HLA-G HISTOCOMPATIBILITY ANTIGEN, CLASS I, G NM_002127 No chr6 29866918 29867384 + 6.4 3.6 No 122 MYC V-MYC MYELOCYTOMATOSIS VIRAL ONCOGENE HOMOLOG NM_002467 No chr8 128877483 128877798 + 6.4 3.0 No (AVIAN) chr8 128311794 128311933 + 4.9 No 123 SERGEF SECRETION REGULATING GUANINE NUCLEOTIDE EXCHANGE NM_012139 No chr11 17991793 17992171-6.4 3.4 No FACTOR 124 RPL10 RIBOSOMAL PROTEIN L10 NM_006013 No chrx 153280440 153280830 + 6.4 3.0 Yes 153280512, 153280509, 153280757 125 TRIM33 KIAA1113 PROTEIN NM_015906 No chr1 114855586 114855759-6.4 3.7 Yes 114855664 chr1 114853692 114853907-5.4 No 126 SOS1 SON OF SEVENLESS HOMOLOG 1 (DROSOPHILA) NM_005633 No chr2 39204318 39204864-6.3 3.5 No 127 UPK3B UROPLAKIN 3B NM_182684 No chr7 76016127 76016314 + 6.3 2.3 No chr7 76017252 76017402 + 4.9 No 128 STIM2 STROMAL INTERACTION MOLECULE 2 NM_020860 No chr4 26469303 26469701 + 6.3 4.8 Yes 26469359 129 RAP2B RAP2B, MEMBER OF RAS ONCOGENE FAMILY NM_002886 No chr3 154360768 154361028 + 6.3 9.5 Yes 154360960, 154360992, 154360998 130 ECE2 ENDOTHELIN CONVERTING ENZYME 2 NM_014693 No chr3 185450903 185451104 + 6.3 4.8 Yes 185450973 131 TCP11L2 T-COMPLEX 11 (MOUSE) LIKE 2 NM_152772 No chr12 105214203 105214510 + 6.2 8.7 Yes 105214310, 105214307 132 PEX13 PEROXISOME BIOGENESIS FACTOR 13 NM_002618 No chr2 61097159 61097553 + 6.2 5.4 Yes 61097500 133 RAPGEF1 RAP GUANINE NUCLEOTIDE EXCHANGE FACTOR (GEF) 1 NM_005312 No chr9 133609729 133610065-6.2 12.0 Yes 133609802, 133609799, 133609921 134 SEPSECS SOLUBLE LIVER ANTIGEN/LIVER PANCREAS ANTIGEN NM_153825 No chr4 24771418 24771735-6.2 5.0 Yes 24771475 135 NFIL3 NUCLEAR FACTOR, INTERLEUKIN 3 REGULATED NM_005384 Yes chr9 93224779 93225137-6.2 5.5 No 136 TRPM7 TRANSIENT RECEPTOR POTENTIAL CATION CHANNEL, NM_017672 No chr15 48766562 48766996-6.2 3.5 Yes 48766848 SUBFAMILY M, MEMBER 7 137 ENO3 ENOLASE 1, (ALPHA) NM_001428 No chr1 8862194 8862868-6.2 3.1 No 138 LOC90342 TRANSFERRIN NM_001077400 No chr2 96709589 96709999 + 6.1 3.3 Yes 96709594 139 LOC399900 HYPOTHETICAL GENE SUPPORTED BY AK093779 NM_001013667 No chr11 61496311 61496994 + 6.1 5.8 Yes 61496808 140 GPRC5A G PROTEIN-COUPLED RECEPTOR, FAMILY C, GROUP 5, NM_003979 Yes chr12 12916493 12916829 + 6.1 11.2 Yes 12916634 MEMBER A 141 C1ORF51 CHROMOSOME 1 OPEN READING FRAME 51 NM_144697 Yes chr1 148519988 148521201 + 6.1 3.0 Yes 148520828, 148520832, 148521064, 148521095, 148521092, 148521171

Genome-wide analysis of HIF DNA-bdg-supplemental material Name chromosome start end Strand Coordates of 148521064, 148521095, 148521092, 148521171 142 PGK1 PHOSPHOGLYCERATE KINASE 1 NM_000291 Yes chrx 77245762 77245920 + 6.1 2.9 No 143 S100A10 S100 CALCIUM BINDING PROTEIN A10 (ANNEXIN II LIGAND, NM_002966 Yes chr1 150231093 150231432-6.0 5.7 No CALPACTIN I, LIGHT POLYPEPTIDE (P11)) 144 PVRL4 POLIOVIRUS RECEPTOR-RELATED 4 NM_030916 Yes chr1 159328557 159329617-6.0 5.9 Yes 159328770, 159329576 145 CABLES1 CDK5 AND ABL ENZYME SUBSTRATE 1 NM_138375 No chr18 18968706 18968986 + 6.0 3.6 Yes 18968758, 18968818 146 ZNF432 ZINC FINGER PROTEIN 432 NM_014650 Yes chr19 57244167 57244519-6.0 3.7 No 147 LOXL2 LYSYL OXIDASE-LIKE 2 NM_002318 Yes chr8 23258117 23258388-6.0 9.4 No chr8 23258999 23259218-5.8 No 148 UGP2 UDP-GLUCOSE PYROPHOSPHORYLASE 2 NM_006759 No chr2 63923104 63923497 + 6.0 4.8 Yes 63923184, 63923193, 63923300 149 EAPP CHROMOSOME 14 OPEN READING FRAME 11 NM_018453 No chr14 34085851 34086123-6.0 5.1 Yes 34085937 150 EIF2C4 ARGONAUTE 4 NM_017629 Yes chr1 36047447 36047843 + 5.9 Yes 36047658 151 FLJ39743 HYPOTHETICAL PROTEIN FLJ39743 NM_182562 No chr15 96875844 96876207-5.9 9.7 Yes 96876152, 96876177 152 REXO1L1 REX1, RNA EXONUCLEASE 1 HOMOLOG (S. CEREVISIAE)-LIKE 1 NM_172239 No chr8 86757803 86758214-5.9 Yes 86757883 chr8 86876763 86877598-5.4 Yes 86876939 chr8 86758749 86759402-5.3 Yes 86758925 chr8 86875928 86876264-5.3 No chr8 86887877 86888180-5.2 No chr8 86746523 86747180-5.0 Yes 86746735 chr8 86874455 86874672-5.0 No chr8 86888750 86889146-5.0 Yes 86888853 chr8 86900867 86901702-4.9 Yes 86901043 chr8 86903213 86903461-4.9 No chr8 86884022 86884837-4.9 Yes 86884356, 86884658, 86884808 chr8 86745831 86745988-4.9 No chr8 86899963 86900332-4.8 Yes 86900001 chr8 86748905 86749368-4.7 No chr8 86742470 86742725-4.6 Yes 86742546, 86742696 chr8 86872356 86872610-4.6 Yes 86872468 chr8 86863808 86864037-4.5 No chr8 86761144 86761324-4.5 Yes 86761291 chr8 86861151 86861331-4.5 No chr8 86865208 86865414-4.5 No chr8 86898539 86898776-4.4 No chr8 86896496 86896714-4.4 Yes 86896572 chr8 86743212 86743458-4.4 No chr8 86762165 86762772-4.4 Yes 86762485 153 RSPH10B HYPOTHETICAL PROTEIN LOC222967 NM_173565 No chr7 6736546 6736990 + 5.9 No 154 HIST2H3C HISTONE 2, H3C NM_021059 No chr1 148079718 148080064-5.9 Yes 148079739, 148080017 chr1 148090109 148090458-5.5 Yes 148090175, 148090453 chr1 148093450 148093882-5.2 Yes 148093462, 148093523, 148093627, 148093650 chr1 148077262 148077956-4.6 Yes 148077712 155 BASP1 BRAIN ABUNDANT, MEMBRANE ATTACHED SIGNAL PROTEIN 1 NM_006317 No chr5 17622940 17623256 + 5.9 5.1 Yes 17622957, 17623237, 17623234 chr5 17642367 17642754 + 5.8 No chr5 17629808 17630018 + 5.8 Yes 17629825 chr5 17619506 17620069 + 5.7 Yes 17619523, 17619803, 17619800 chr5 17616072 17616536 + 5.6 Yes 17616089, 17616369, 17616366 chr5 17632978 17633558 + 5.2 Yes 17633055, 17633259, 17633539, 17633536 Supplemental material Page 7

Genome-wide analysis of HIF DNA-bdg-supplemental material Name chromosome start end Strand Coordates of 17633536 chr5 17618374 17618717 + 5.1 No chr5 17637383 17637883 + 5.1 Yes 17637861 chr5 17640853 17641317 + 5.1 Yes 17641295 chr5 17621763 17622151 + 4.9 No chr5 17623755 17624111 + 4.8 No chr5 17636676 17637140 + 4.5 Yes 17636693, 17636973, 17636970 chr5 17632148 17632417 + 4.4 No chr5 17616887 17617205 + 4.4 No chr5 17635499 17635870 + 4.1 No 156 ATP8B4 ATPASE, CLASS I, TYPE 8B, MEMBER 4 NM_024837 No chr15 48203265 48203392-5.8 4.3 No 157 RP11-191L9.1 FLJ46257 PROTEIN NM_001001693 No chr22 46406282 46406753-5.8 5.6 No 158 TMEM45A TRANSMEMBRANE PROTEIN 45A NM_018004 Yes chr3 101694373 101695020 + 5.8 5.1 Yes 101694475, 101694897 chr3 101693082 101693469 + 4.5 Yes 101693218 159 MTERFD2 MTERF DOMAIN CONTAINING 2 NM_182501 No chr2 241696995 241697196-5.8 3.2 No 160 RAB24 RAB24, MEMBER RAS ONCOGENE FAMILY NM_001031677 No chr5 176631165 176631409-5.8 5.4 Yes 176631223, 176631220 161 TTC26 HYPOTHETICAL PROTEIN FLJ12571 NM_024926 No chr7 138468526 138468741 + 5.8 3.4 No 162 RNF145 HYPOTHETICAL PROTEIN FLJ31951 NM_144726 No chr5 158567139 158567355-5.8 No 163 SAP18 SIN3A-ASSOCIATED PROTEIN, 18KDA NM_005870 No chr13 20612021 20612324 + 5.8 4.0 Yes 20612304 164 BCAS3 BREAST CARCINOMA AMPLIFIED SEQUENCE 3 NM_017679 No chr17 56111441 56111887 + 5.7 3.9 Yes 56111684, 56111880 chr17 56110825 56111044 + 5.4 No chr17 56157351 56157666 + 5.3 No 165 SRGAP2 SMALL NUCLEAR RNA ACTIVATING COMPLEX, POLYPEPTIDE NM_001042758 No chr1 204625799 204625997 + 5.7 No 3, 50KDA 166 WDR89 CHROMOSOME 14 OPEN READING FRAME 150 NM_001008726 No chr14 63177872 63178106-5.7 3.2 No 167 LOC402164 DEUBIQUITINATING ENZYME 3 NM_201402 No chr4 8973704 8974332 + 5.6 Yes 8974220, 8974297 chr4 8954580 8955351 + 5.6 Yes 8955239, 8955316 chr4 8965775 8967512 + 5.5 Yes 8966080, 8966388, 8966964, 8967187 chr4 8961687 8963293 + 5.4 Yes 8962219, 8962442, 8963195 chr4 8968815 8969515 + 5.3 Yes 8969474 chr4 8970587 8972041 + 5.3 Yes 8970825, 8971133, 8971709, 8971932 chr4 8957005 8958144 + 5.2 Yes 8957474, 8957697 chr4 8959325 8960096 + 5.2 Yes 8959984, 8960061 chr4 8964140 8964698 + 5.2 No chr4 8975923 8977565 + 5.1 Yes 8976455, 8976678, 8977431 chr4 8952224 8953755 + 5.0 Yes 8952729, 8952952, 8953705 chr4 8975333 8975485 + 4.8 No chr4 8978185 8979337 + 4.8 Yes 8978965, 8979042, 8979121 chr4 8960827 8961249 + 4.5 No chr4 8956184 8956504 + 4.4 No 168 PARD6B PAR-6 PARTITIONING DEFECTIVE 6 HOMOLOG BETA (C. NM_032521 No chr20 48779653 48780022 + 5.6 4.2 No ELEGANS) chr20 48782141 48782590 + 5.5 No chr20 48777953 48778125 + 4.2 Yes 48777991 169 STARD4 START DOMAIN CONTAINING 4, STEROL REGULATED NM_139164 No chr5 110876389 110876601-5.6 3.1 No 170 LOC440350 SIMILAR TO NUCLEAR PORE COMPLEX INTERACTING NM_001018122 No chr16 28389569 28389929-5.6 3.2 Yes 28389651 PROTEIN chr16 28676970 28677200-5.2 No 171 GAGE1 G ANTIGEN 1 NM_001468 No chrx 49252884 49253018 + 5.6 No 172 DHX35 DEAH (ASP-GLU-ALA-HIS) BOX POLYPEPTIDE 35 NM_021931 No chr20 37022424 37022756 + 5.6 12.7 No Supplemental material Page 8

Genome-wide analysis of HIF DNA-bdg-supplemental material Name chromosome start end Strand Coordates of 173 ALDOC ALDOLASE C, FRUCTOSE-BISPHOSPHATE NM_005165 Yes chr17 23927723 23927967-5.6 4.4 No 174 NCOA5 NUCLEAR RECEPTOR COACTIVATOR 5 NM_020967 No chr20 44152130 44152413-5.6 Yes 44152356, 44152353 175 MINK1 MISSHAPEN-LIKE KINASE 1 (ZEBRAFISH) NM_001024937 No chr17 4682194 4682642 + 5.6 6.0 No 176 NLRP4 NACHT, LEUCINE RICH REPEAT AND PYD CONTAINING 4 NM_134444 No chr19 61053442 61054771 + 5.6 No 177 GPR1 G PROTEIN-COUPLED RECEPTOR 1 NM_005279 No chr2 206848525 206848691-5.6 2.8 Yes 206848547, 206848671 178 C3ORF14 CHROMOSOME 3 OPEN READING FRAME 14 NM_020685 No chr3 62280523 62280960 + 5.6 4.4 No 179 SYTL2 SYNAPTOTAGMIN-LIKE 2 NM_206929 Yes chr11 85108041 85108210-5.6 3.9 Yes 85108059 180 NACA2 NASCENT-POLYPEPTIDE-ASSOCIATED COMPLEX ALPHA POLYPEPTIDE-LIKE NM_199290 No chr17 57028123 57028720-5.5 No chr17 57021911 57023001-5.0 Yes 57022784 181 FLJ39739 FLJ39739 PROTEIN NM_207400 Yes chr1 146398200 146398416-5.5 4.7 Yes 146398248, 146398285 chr1 146396717 146397303-4.9 Yes 146396889, 146396971, 146396984, 146397180 182 ZNF107 ZINC FINGER PROTEIN 588 NM_001013746 No chr7 63784379 63784552 + 5.5 No 183 IRF2BP2 TRANSFERRIN NM_001077397 No chr1 232813966 232814367-5.5 6.8 No 184 PDGFB PLATELET-DERIVED GROWTH FACTOR BETA POLYPEPTIDE NM_002608 Yes chr22 37978478 37978860-5.5 7.0 No (SIMIAN SARCOMA VIRAL (V-SIS) ONCOGENE HOMOLOG) 185 AMAC1L2 ACYL-MALONYL CONDENSING ENZYME 1-LIKE 2 NM_054028 No chr8 11256606 11256937 + 5.5 7.0 No 186 RABL2A RAB, MEMBER OF RAS ONCOGENE FAMILY-LIKE 2A NM_007082 No chr2 114126889 114127617 + 5.5 3.2 No chr2 114124976 114125955 + 4.5 No chr2 114060255 114060389 + 4.0 No 187 NBPF1 3-OXOACYL-ACP SYNTHASE, MITOCHONDRIAL NM_017940 No chr1 147160785 147161102-5.5 3.1 No chr1 147171348 147171708-5.1 No 188 ANKZF1 SMALL NUCLEAR RNA ACTIVATING COMPLEX, POLYPEPTIDE 3, 50KDA NM_001042410 Yes chr2 219803046 219803691 + 5.5 Yes 219803180, 219803395, 219803579 189 JARID1B JUMONJI, AT RICH INTERACTIVE DOMAIN 1B (RBP2-LIKE) NM_006618 No chr1 201047816 201048139-5.4 No 190 SORT1 SORTILIN 1 NM_002959 No chr1 109742951 109743267-5.4 3.3 Yes 109743059 191 WDR54 WD REPEAT DOMAIN 54 NM_032118 Yes chr2 74502413 74502613 + 5.4 No 192 CSTF1 CLEAVAGE STIMULATION FACTOR, 3' PRE-RNA, SUBUNIT 1, NM_001033522 No chr20 54401333 54401553 + 5.4 No 50KDA 193 ATP9A ATPASE, CLASS II, TYPE 9A NM_006045 No chr20 49816815 49816993-5.4 4.1 No 194 WISP2 WNT1 INDUCIBLE SIGNALING PATHWAY PROTEIN 2 NM_003881 Yes chr20 42778686 42778864 + 5.4 5.7 No 195 BMP7 BONE MORPHOGENETIC PROTEIN 7 (OSTEOGENIC PROTEIN 1) NM_001719 No chr20 55277770 55278171-5.4 4.4 No 196 ENO2 ENOLASE 2 (GAMMA, NEURONAL) NM_001975 Yes chr12 6893566 6893800 + 5.4 4.4 No 197 PFKFB4 6-PHOSPHOFRUCTO-2-KINASE/FRUCTOSE-2,6-BIPHOSPHATASE NM_004567 Yes chr3 48570336 48570633-5.4 2.6 No 4 198 PPP2R1A PROTEIN PHOSPHATASE 2 (FORMERLY 2A), REGULATORY NM_014225 No chr19 57384271 57384661 + 5.4 4.4 No SUBUNIT A (PR 65), ALPHA ISOFORM 199 TMOD3 TROPOMODULIN 3 (UBIQUITOUS) NM_014547 No chr15 49909868 49910085 + 5.4 4.9 Yes 49909906 200 ID2 INHIBITOR OF DNA BINDING 2, DOMINANT NEGATIVE HELIX- NM_002166 No chr2 8735865 8736101 + 5.4 5.5 No LOOP-HELIX PROTEIN 201 PSMA1 PROTEASOME (PROSOME, MACROPAIN) SUBUNIT, ALPHA NM_002786 No chr11 14498905 14499265-5.4 No TYPE, 1 202 PGAM1 PHOSPHOGLYCERATE MUTASE 1 (BRAIN) NM_002629 No chr10 99175133 99175390 + 5.4 2.4 Yes 99175252, 99175348 203 GIYD2 GIY-YIG DOMAIN CONTAINING 2 NM_001014999 No chr16 29305154 29305676 + 5.4 No chr16 29306183 29306638 + 5.3 No 204 PPIAL4 PEPTIDYLPROLYL ISOMERASE A (CYCLOPHILIN A)-LIKE 4 NM_178230 No chr1 142932381 142933042-5.4 2.2 No chr1 143079011 143079295-5.3 Yes 143079194 chr1 146421298 146421515-4.8 No chr1 142934552 142934939-4.4 No chr1 143074858 143075075-4.3 No 205 TGIF1 TGFB-INDUCED FACTOR (TALE FAMILY HOMEOBOX) NM_173209 No chr18 3438820 3439039 + 5.3 4.4 No 206 SPAG9 SPERM ASSOCIATED ANTIGEN 9 NM_003971 No chr17 46553768 46554543-5.3 4.0 Yes 46554297, 46554294, 46554322 207 HIST2H2BF HISTONE 2, H2BF NM_001024599 No chr1 148050453 148051097-5.3 2.7 No 208 RIT1 RAS-LIKE WITHOUT CAAX 1 NM_006912 No chr1 154148103 154148331-5.3 3.9 No 209 SULT1A4 SULFOTRANSFERASE FAMILY, CYTOSOLIC, 1A, PHENOL- NM_001017390 No chr16 30147728 30148042 + 5.3 No PREFERRING, MEMBER 3 210 MYNN MYONEURIN NM_018657 No chr3 170972528 170973078 + 5.3 Yes 170972836, 170973011, 170973008 211 AKAP13 LYMPHOID BLAST CRISIS ONCOGENE NM_006738 No chr15 83579433 83579723 + 5.3 3.8 Yes 83579676 212 ZNF318 ZINC FINGER PROTEIN 318 NM_014345 No chr6 43445727 43445878-5.3 No 213 RELT TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY, MEMBER 19-LIKE NM_032871 No chr11 72765920 72766169 + 5.3 4.9 Yes 72765939 Supplemental material Page 9

Genome-wide analysis of HIF DNA-bdg-supplemental material Name chromosome start end Strand Coordates of 214 GRB2 GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2 NM_002086 No chr17 70914096 70914320-5.3 2.7 No 215 ESM1 ENDOTHELIAL CELL-SPECIFIC MOLECULE 1 NM_007036 No chr5 54319361 54319508-5.3 3.4 No 216 SMURF2 SMAD SPECIFIC E3 UBIQUITIN PROTEIN LIGASE 2 NM_022739 No chr17 60087738 60087894-5.3 3.9 No 217 AXUD1 AXIN1 UP-REGULATED 1 NM_033027 No chr3 39169182 39169354-5.3 9.0 Yes 39169192, 39169244, 39169268, 39169284 218 IPMK INOSITOL POLYPHOSPHATE MULTIKINASE NM_152230 No chr10 59696165 59696646-5.3 4.4 Yes 59696561, 59696612 219 UQCRC2 UBIQUINOL-CYTOCHROME C REDUCTASE CORE PROTEIN II NM_003366 No chr16 21770233 21770647 + 5.3 4.1 Yes 21770315, 21770327 chr16 21759713 21759849 + 4.9 No 220 KIAA1715 KIAA1715 NM_030650 Yes chr2 176574234 176574603-5.3 3.4 Yes 176574488, 176574587, 176574596 221 COX7C CYTOCHROME C OXIDASE SUBUNIT VIIC NM_001867 No chr5 85616114 85616439 + 5.3 7.6 No 222 SMEK2 KIAA1387 PROTEIN NM_020463 No chr2 55698553 55698820-5.3 3.9 Yes 55698566, 55698774 223 PODXL PODOCALYXIN-LIKE NM_001018111 No chr7 130997216 130997467-5.3 3.0 No 224 CCT8L2 T-COMPLEX PROTEIN 1 NM_014406 No chr22 15464577 15464981-5.2 2.8 Yes 15464837 225 PSMD6 PROTEASOME (PROSOME, MACROPAIN) 26S SUBUNIT, NON- ATPASE, 6 226 SPRY1 SPROUTY HOMOLOG 1, ANTAGONIST OF FGF SIGNALING (DROSOPHILA) NM_014814 No chr3 63991402 63991840-5.2 Yes 63991595, 63991664 chr3 63983613 63983759-4.4 No NM_199327 Yes chr4 124537498 124538111 + 5.2 5.6 Yes 124537860, 124538022, 124538063 227 SMAP1L STROMAL MEMBRANE-ASSOCIATED PROTEIN 1-LIKE NM_022733 No chr1 40613035 40613415 + 5.2 No 228 TNIP1 TNFAIP3 INTERACTING PROTEIN 1 NM_006058 No chr5 150441328 150441809-5.2 4.8 No 229 FBL FIBRILLARIN NM_001436 No chr19 45029826 45030200-5.2 3.2 No 230 RAD51C RAD51 HOMOLOG C (S. CEREVISIAE) NM_002876 No chr17 54128826 54129068 + 5.2 No 231 OPN1MW OPSIN 1 (CONE PIGMENTS), MEDIUM-WAVE-SENSITIVE NM_000513 No chrx 153102567 153102780 + 5.2 4.5 No (COLOR BLINDNESS, DEUTAN) 232 FAM103A1 FAMILY WITH SEQUENCE SIMILARITY 103, MEMBER A1 NM_031452 No chr15 81445340 81445527 + 5.2 No 233 C10ORF28 CHROMOSOME 10 OPEN READING FRAME 28 NM_014472 No chr10 99884069 99884289 + 5.2 Yes 99884200 234 FER1L3 FER-1-LIKE 3, MYOFERLIN (C. ELEGANS) NM_013451 No chr10 95186981 95187309-5.1 6.1 Yes 95187175 235 ATXN1 ATAXIN 1 NM_000332 Yes chr6 16874305 16874530-5.1 5.1 No 236 KIAA0460 KIAA0460 NM_015203 No chr1 148604264 148604625 + 5.1 3.7 Yes 148604375 237 GAGE6 G ANTIGEN 6 NM_001476 No chrx 49233573 49233796 + 5.1 3.4 No chrx 49223851 49224392 + 5.0 No chrx 49209481 49210125 + 5.0 Yes 49209934, 49210113 chrx 49219434 49219684 + 4.8 Yes 49219493, 49219672 chrx 49207983 49208243 + 4.6 Yes 49208210 chrx 49185669 49185837 + 4.5 No 238 BCKDHA BRANCHED CHAIN KETO ACID DEHYDROGENASE E1, ALPHA NM_000709 No chr19 46595493 46595714 + 5.1 2.6 Yes 46595535 POLYPEPTIDE 239 GREB1 GREB1 PROTEIN NM_014668 No chr2 11590641 11590824 + 5.1 No 240 TARS THREONYL-TRNA SYNTHETASE NM_152295 No chr5 33475595 33476108 + 5.1 3.7 Yes 33476046, 33476064 241 FANK1 FIBRONECTIN TYPE III AND ANKYRIN REPEAT DOMAINS 1 NM_145235 Yes chr10 127598292 127598486 + 5.1 No 242 PLA2G10 PHOSPHOLIPASE A2, GROUP X NM_003561 No chr16 14713206 14713486-5.1 3.4 No chr16 14752397 14752648-4.8 No 243 DAAM1 DISHEVELLED ASSOCIATED ACTIVATOR OF MORPHOGENESIS NM_014992 Yes chr14 58674101 58674282 + 5.1 No 1 244 ATP11A ATPASE, CLASS VI, TYPE 11A NM_015205 No chr13 112481053 112481541 + 5.1 No 245 NDUFB9 NADH DEHYDROGENASE (UBIQUINONE) 1 BETA NM_005005 No chr8 125657057 125657227 + 5.1 2.7 No SUBCOMPLEX, 9, 22KDA 246 HEATR6 AMPLIFIED IN BREAST CANCER 1 NM_022070 No chr17 55454775 55455126-5.1 No chr17 55513062 55513314-4.6 Yes 55513128 247 TPT1 TUMOR PROTEIN, TRANSLATIONALLY-CONTROLLED 1 NM_003295 No chr13 44814050 44814233-5.1 No 248 ZNF323 ZINC FINGER PROTEIN 323 NM_030899 No chr6 28410668 28410850-5.1 Yes 28410765 249 PAK7 P21(CDKN1A)-ACTIVATED KINASE 7 NM_020341 No chr20 9770334 9770510-5.1 No 250 MXI1 MAX INTERACTOR 1 NM_001008541 Yes chr10 111959419 111959567 + 5.1 5.1 Yes 111959493 251 ANLN ANILLIN, ACTIN BINDING PROTEIN (SCRAPS HOMOLOG, NM_018685 No chr7 36393613 36393788 + 5.1 3.7 No DROSOPHILA) 252 TUBD1 TUBULIN, DELTA 1 NM_016261 No chr17 55324332 55324849-5.1 Yes 55324826 253 TBX4 T-BOX 4 NM_018488 No chr17 56884994 56885248 + 5.1 No 254 MTMR11 MYOTUBULARIN RELATED PROTEIN 11 NM_181873 No chr1 148175740 148176042-5.1 3.3 Yes 148176020 255 RASSF3 RAS ASSOCIATION (RALGDS/AF-6) DOMAIN FAMILY 3 NM_178169 No chr12 63289103 63289250 + 5.1 2.9 No 256 HFE2 HEMOCHROMATOSIS TYPE 2 (JUVENILE) NM_213653 No chr1 144027850 144028288 + 5.0 2.5 Yes 144028012 chr1 144028822 144030110 + 4.7 Yes 144029574, 144029830 Supplemental material Page 10

Genome-wide analysis of HIF DNA-bdg-supplemental material Name chromosome start end Strand Coordates of chr1 144024672 144025390 + 4.5 Yes 144024854 chr1 144025985 144026681 + 4.5 Yes 144026424 chr1 144027129 144027433 + 4.4 No 257 ZNF250 ZINC FINGER PROTEIN 250 NM_021061 No chr8 146096728 146096878-5.0 4.1 No 258 HIPK1 KIAA0630 PROTEIN NM_181358 Yes chr1 114298931 114299161 + 5.0 No 259 BCAS4 BREAST CARCINOMA AMPLIFIED SEQUENCE 4 NM_017843 No chr20 48844060 48844378 + 5.0 No 260 METTL9 TRANSFERRIN NM_001077180 No chr16 21437014 21437155 + 5.0 3.3 No 261 BRIP1 BRCA1 INTERACTING PROTEIN C-TERMINAL HELICASE 1 NM_032043 No chr17 57294924 57295174-5.0 No 262 PPM1D PROTEIN PHOSPHATASE 1D MAGNESIUM-DEPENDENT, DELTA NM_003620 No chr17 56031494 56031820 + 5.0 2.5 No ISOFORM 263 LOC198437 BA299N6.3 NM_001007125 No chr20 62189016 62189300-5.0 3.9 No 264 CCRL1 CHEMOKINE (C-C MOTIF) RECEPTOR-LIKE 1 NM_178445 No chr3 133802444 133802579 + 5.0 3.6 No 265 ANXA2 ANNEXIN A2 NM_001002857 No chr15 58478749 58478894-5.0 2.9 Yes 58478804, 58478810 266 TRIM27 RET FINGER PROTEIN NM_006510 No chr6 28972352 28972548-5.0 4.1 No 267 ITFG2 UNCHARACTERIZED HEMATOPOIETIC STEM/PROGENITOR NM_018463 No chr12 2792803 2793011 + 5.0 No CELLS PROTEIN MDS028 268 CLK2 CDC-LIKE KINASE 2 NM_003993 No chr1 153508941 153509122-5.0 2.8 No 269 CTGLF1 CENTAURIN, GAMMA-LIKE FAMILY, MEMBER 1 NM_133446 No chr10 45670125 45670374-5.0 3.8 No 270 LOC440888 FKSG73 PROTEIN NM_001032412 No chr2 91431042 91431257 + 5.0 2.6 No chr2 91426182 91426328 + 4.7 No chr2 91040298 91040620 + 4.6 No 271 FLJ44005 FLJ44005 PROTEIN NM_001001689 No chr1 176741457 176741665-5.0 No 272 CDK2AP1 CDK2-ASSOCIATED PROTEIN 1 NM_004642 No chr12 122322638 122323058-5.0 3.7 Yes 122322693 273 ZFHX3 AT-BINDING TRANSCRIPTION FACTOR 1 NM_006885 No chr16 71646053 71646245-4.9 No 274 GOLGA GOLGIN-LIKE PROTEIN NM_018652 No chr15 70735414 70735795 + 4.9 Yes 70735583 275 KIAA1920 KIAA1920 PROTEIN NM_052919 No chr15 82688509 82688752-4.9 2.8 No chr15 82517695 82517889-4.6 No 276 HNRPD HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN D (AU- NM_001003810 No chr4 83512876 83513050-4.9 7.6 No RICH ELEMENT RNA BINDING PROTEIN 1, 37KDA) 277 BTBD3 BTB (POZ) DOMAIN CONTAINING 3 NM_181443 No chr20 11820353 11820684 + 4.9 3.1 No 278 C5ORF36 HYPOTHETICAL PROTEIN MGC34713 NM_173665 No chr5 93972643 93972792-4.9 3.5 No 279 RAB6IP1 RAB6 INTERACTING PROTEIN 1 NM_015213 No chr11 9242658 9242848-4.9 Yes 9242735 280 HJURP HYPOTHETICAL PROTEIN DKFZP762E1312 NM_018410 No chr2 234436003 234436307-4.9 No 281 CLASP1 CYTOPLASMIC LINKER ASSOCIATED PROTEIN 1 NM_015282 No chr2 122125014 122125184-4.9 3.4 No 282 C1ORF147 CHROMOSOME 1 OPEN READING FRAME 147 NM_001025592 No chr1 204739101 204739236-4.9 3.1 No 283 CLTC CLATHRIN, HEAVY POLYPEPTIDE (HC) NM_004859 No chr17 55051037 55051214 + 4.9 No 284 DOK5 DOCKING PROTEIN 5 NM_018431 No chr20 52526530 52526755 + 4.9 Yes 52526616 285 FEZF2 ZINC FINGER PROTEIN 312 NM_018008 No chr3 62441575 62441707-4.9 No 286 PKM2 PYRUVATE KINASE, MUSCLE NM_002654 No chr15 70308614 70308764-4.9 2.9 No 287 PRICKLE3 LIM DOMAIN ONLY 6 NM_006150 No chrx 48930115 48930281-4.9 2.7 No 288 TREM1 TRIGGERING RECEPTOR EXPRESSED ON MYELOID CELLS 1 NM_018643 No chr6 41363777 41363979-4.9 5.0 No 289 EDEM1 ER DEGRADATION ENHANCER, MANNOSIDASE ALPHA-LIKE 1 NM_014674 No chr3 5203655 5203902 + 4.9 4.2 Yes 5203697 290 OR4A47 OLFACTORY RECEPTOR, FAMILY 4, SUBFAMILY A, MEMBER NM_001005512 No chr11 48469350 48469487 + 4.9 2.4 No 47 291 YEATS2 YEATS DOMAIN CONTAINING 2 NM_018023 Yes chr3 184899640 184899779 + 4.9 3.0 No 292 LOC497190 SECRETORY PROTEIN LOC497190 NM_001011880 No chr16 72957808 72957997-4.9 2.7 No 293 AP4B1 ADAPTOR-RELATED PROTEIN COMPLEX 4, BETA 1 SUBUNIT NM_006594 No chr1 114244644 114244944-4.9 2.8 No 294 SLN SARCOLIPIN NM_003063 No chr11 107112485 107112696-4.9 Yes 107112619 295 LOC441242 HYPOTHETICAL LOC441242 NM_001013464 No chr7 64750993 64751194-4.9 Yes 64751043 chr7 64751863 64752076-4.8 Yes 64751880 296 NDUFA5 NADH DEHYDROGENASE (UBIQUINONE) 1 ALPHA NM_005000 No chr7 122983840 122984123-4.9 No SUBCOMPLEX, 5, 13KDA 297 OR4F3 OLFACTORY RECEPTOR, FAMILY 4, SUBFAMILY F, MEMBER 3 NM_001005221 No chr1 223059 223204 + 4.9 3.4 No 298 PLOD3 PROCOLLAGEN-LYSINE, 2-OXOGLUTARATE 5-DIOXYGENASE NM_001084 No chr7 100647759 100647962-4.9 6.0 No 3 299 HSPBAP1 HSPB (HEAT SHOCK 27KDA) ASSOCIATED PROTEIN 1 NM_024610 No chr3 123994018 123994159-4.9 No 300 NBPF15 NEUROBLASTOMA BREAKPOINT FAMILY, MEMBER 14 NM_183372 No chr1 144929740 144930109-4.8 2.9 No chr1 144927863 144928164-4.4 Yes 144927885 chr1 144931522 144932121-4.3 No 301 GUSBP1 HYPOTHETICAL PROTEIN LOC153561 NM_207331 Yes chr5 69174606 69174858 + 4.8 4.9 No 302 OR7A17 OLFACTORY RECEPTOR, FAMILY 7, SUBFAMILY A, MEMBER NM_030901 No chr19 14867841 14867993-4.8 5.4 Yes 14867954 17 303 NFATC4 NUCLEAR FACTOR OF ACTIVATED T-CELLS, CYTOPLASMIC, NM_004554 No chr14 23905936 23906167 + 4.8 3.2 No CALCINEURIN-DEPENDENT 4 304 AZI2 5-AZACYTIDINE INDUCED 2 NM_022461 Yes chr3 28364552 28364719-4.8 4.8 Yes 28364575 305 PLEKHA6 PLECKSTRIN HOMOLOGY DOMAIN CONTAINING, FAMILY A NM_014935 No chr1 202599695 202599991-4.8 5.6 Yes 202599718 MEMBER 6 306 CDR2 CEREBELLAR DEGENERATION-RELATED PROTEIN 2, 62KDA NM_001802 No chr16 22446378 22446584-4.8 No chr16 22448973 22449291-4.8 No chr16 22450730 22451056-4.2 Yes 22450893 307 MAP3K13 MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 13 NM_004721 Yes chr3 186563826 186564323 + 4.8 Yes 186564066, 186564098 Supplemental material Page 11

Genome-wide analysis of HIF DNA-bdg-supplemental material Name chromosome start end Strand Coordates of 308 TBXAS1 THROMBOXANE A SYNTHASE 1 (PLATELET, CYTOCHROME NM_030984 No chr7 139120473 139120615 + 4.8 Yes 139120537 P450, FAMILY 5, SUBFAMILY A) 309 ELMO2 ENGULFMENT AND CELL MOTILITY 2 NM_133171 No chr20 44518895 44519115-4.8 3.6 No 310 TFB1M TRANSCRIPTION FACTOR B1, MITOCHONDRIAL NM_016020 No chr6 155677984 155678144-4.8 3.6 No 311 GAGE8 G ANTIGEN 8 NM_012196 No chrx 49067407 49067720 + 4.8 No 312 NBN NIBRIN NM_001024688 No chr8 91070473 91070750-4.8 3.2 No chr8 91065093 91065316-4.7 No 313 TMEM121 TRANSMEMBRANE PROTEIN 121 NM_025268 No chr14 105131849 105132071 + 4.8 3.0 No chr14 105659527 105659694 + 4.7 Yes 105659640, 105659673 chr14 105131037 105131388 + 4.1 No 314 CCDC47 COILED-COIL DOMAIN CONTAINING 47 NM_020198 No chr17 59203697 59204084-4.7 3.8 No 315 GGT3 GAMMA-GLUTAMYLTRANSFERASE 2 NM_002058 No chr22 19985953 19986100-4.7 2.9 No 316 PAIP2 POLY(A) BINDING PROTEIN INTERACTING PROTEIN 2 NM_016480 No chr5 138704920 138705115 + 4.7 3.0 Yes 138704974, 138705108 317 NCOA7 NUCLEAR RECEPTOR COACTIVATOR 7 NM_181782 No chr6 126143751 126143902 + 4.7 5.0 Yes 126143766 318 SLC45A3 SOLUTE CARRIER FAMILY 45, MEMBER 3 NM_033102 Yes chr1 203900075 203900281-4.7 5.9 No 319 VAC14 TAX1 (HUMAN T-CELL LEUKEMIA VIRUS TYPE I) BINDING NM_018052 No chr16 69452671 69452911-4.7 3.0 No PROTEIN 2 320 GAPDH GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE NM_002046 Yes chr12 6513390 6513563 + 4.7 4.1 Yes 6513523 321 DHX40 DEAH (ASP-GLU-ALA-HIS) BOX POLYPEPTIDE 40 NM_024612 No chr17 54993599 54993781 + 4.7 No 322 DSP DESMOPLAKIN NM_001008844 Yes chr6 7486301 7486474 + 4.7 4.0 Yes 7486427 323 C1QTNF3 COMPLEMENT-C1Q TUMOR NECROSIS FACTOR-RELATED NM_030945 No chr5 34215412 34215547-4.7 2.3 Yes 34215460 PROTEIN; LIKELY ORTHOLOG OF MOUSE CORS26 (COLLAGENOUS REPEAT-CONTAINING SEQUENCE OF 26-KDA PROTEIN) chr5 34214826 34215037-4.4 No 324 LOC283755 HYPOTHETICAL PROTEIN LOC283755 NM_001024682 No chr15 18998125 18998387-4.7 3.1 No 325 PLOD2 PROCOLLAGEN-LYSINE, 2-OXOGLUTARATE 5-DIOXYGENASE NM_000935 Yes chr3 147360830 147361005-4.7 4.6 No 2 chr3 147362257 147362515-4.5 Yes 147362330, 147362398 326 RUNX1 RUNT-RELATED TRANSCRIPTION FACTOR 1 (ACUTE MYELOID NM_001001890 Yes chr21 35181544 35181752-4.7 6.8 No LEUKEMIA 1; AML1 ONCOGENE) 327 GLRX GLUTAREDOXIN (THIOLTRANSFERASE) NM_002064 Yes chr5 95184993 95185174-4.7 No 328 HSDL2 HYDROXYSTEROID DEHYDROGENASE LIKE 2 NM_032303 No chr9 114182599 114182734 + 4.7 3.9 Yes 114182604 329 PSMD7 PROTEASOME (PROSOME, MACROPAIN) 26S SUBUNIT, NON- NM_002811 No chr16 72889077 72889211 + 4.7 No ATPASE, 7 (MOV34 HOMOLOG) 330 TEX2 TESTIS EXPRESSED SEQUENCE 2 NM_018469 No chr17 59746168 59746425-4.7 3.1 No 331 CYP24A1 CYTOCHROME P450, FAMILY 24, SUBFAMILY A, POLYPEPTIDE NM_000782 No chr20 52221508 52222118-4.7 No 1 332 RPS17 RIBOSOMAL PROTEIN S17 NM_001021 No chr15 80584050 80584272-4.6 3.3 No 333 CA9 CARBONIC ANHYDRASE IX NM_001216 Yes chr9 35663227 35663406 + 4.6 No 334 NCBP1 NUCLEAR CAP BINDING PROTEIN SUBUNIT 1, 80KDA NM_002486 No chr9 99434824 99435027 + 4.6 3.2 No 335 DGKH DIACYLGLYCEROL KINASE, ETA NM_152910 No chr13 41513691 41513869 + 4.6 2.9 No 336 KRTCAP3 KERATINOCYTE ASSOCIATED PROTEIN 3 NM_173853 No chr2 27515360 27515532 + 4.6 3.0 No 337 TRAF7 TNF RECEPTOR-ASSOCIATED FACTOR 7 NM_206835 No chr16 2154433 2154596 + 4.6 2.6 Yes 2154504, 2154586 338 FAM84B FAMILY WITH SEQUENCE SIMILARITY 84, MEMBER B NM_174911 No chr8 127637221 127637377-4.6 2.6 No 339 ZNF217 ZINC FINGER PROTEIN 217 NM_006526 No chr20 51632609 51632926-4.6 3.2 No chr20 51635534 51635790-4.5 No 340 KRTAP5-7 KERATIN ASSOCIATED PROTEIN 5-7 NM_001012503 No chr11 70911239 70911511 + 4.6 3.7 Yes 70911245, 70911280, 70911315, 70911350, 70911385, 70911420 341 SMCR7 SMITH-MAGENIS SYNDROME CHROMOSOME REGION, NM_139162 No chr17 18103947 18104097 + 4.6 No CANDIDATE 7 342 BCAS1 BREAST CARCINOMA AMPLIFIED SEQUENCE 1 NM_003657 No chr20 52120625 52120824-4.6 3.0 Yes 52120802 chr20 51925581 51925844-4.5 No chr20 51926630 51926810-4.2 No 343 C17ORF64 CHROMOSOME 17 OPEN READING FRAME 64 NM_181707 No chr17 55867461 55867679 + 4.6 No 344 RIPK4 RECEPTOR-INTERACTING SERINE-THREONINE KINASE 4 NM_020639 Yes chr21 42107930 42108493-4.6 2.3 No 345 MPV17L MPV17-LIKE PROTEIN TYPE 2 NM_173803 No chr16 15379258 15379507 + 4.6 No 346 TMTC2 TRANSMEMBRANE AND TETRATRICOPEPTIDE REPEAT CONTAINING 2 NM_152588 Yes chr12 81604071 81604350 + 4.6 5.7 Yes 81604210, 81604327 347 RLF REARRANGED L-MYC FUSION NM_012421 Yes chr1 40400357 40400729 + 4.6 No 348 ZFP14 MOUSE ZINC FINGER PROTEIN 14-LIKE NM_020917 No chr19 41487904 41488049-4.6 Yes 41487956 349 FOXD4 FORKHEAD BOX D4 NM_207305 No chr9 70441 70662-4.5 No 350 PFDN4 PREFOLDIN SUBUNIT 4 NM_002623 No chr20 52266407 52266553 + 4.5 No 351 C15ORF39 DKFZP434H132 PROTEIN NM_015492 No chr15 73339506 73339726 + 4.5 3.6 No chr15 73336273 73336451 + 4.4 No Supplemental material Page 12

Genome-wide analysis of HIF DNA-bdg-supplemental material Name chromosome start end Strand Coordates of 352 HSD17B3 HYDROXYSTEROID (17-BETA) DEHYDROGENASE 3 NM_000197 No chr9 97948943 97949108-4.5 Yes 97949073 353 ERGIC2 ERGIC AND GOLGI 2 NM_016570 No chr12 29425599 29425781-4.5 3.7 No 354 TP53 TUMOR PROTEIN P53 (LI-FRAUMENI SYNDROME) NM_000546 No chr17 7530206 7530476-4.5 2.6 No 355 DKFZP434K191 HYPOTHETICAL PROTEIN DKFZP434K191 NM_001029950 No chr22 17233196 17233345 + 4.5 No 356 RUNDC2B RUN DOMAIN CONTAINING 2A NM_001012391 No chr16 21338020 21338330 + 4.5 Yes 21338035, 21338047 357 NOMO3 NODAL MODULATOR 3 NM_001004067 No chr16 16347627 16347951 + 4.5 2.7 No chr16 16350605 16350738 + 4.1 No 358 TUBA3C TUBULIN, ALPHA 2 NM_006001 No chr13 18610123 18610343-4.5 No 359 FOXD4L1 FORKHEAD BOX D4-LIKE 1 NM_012184 No chr2 114008587 114008741 + 4.5 No chr2 113966691 113966922 + 4.4 No 360 FLJ22795 HYPOTHETICAL PROTEIN FLJ22795 NM_025084 No chr15 80982669 80982809-4.5 No 361 ZNF295 ZINC FINGER PROTEIN 295 NM_020727 No chr21 42305354 42305590-4.5 3.5 No 362 NBPF10 SMALL NUCLEAR RNA ACTIVATING COMPLEX, POLYPEPTIDE NM_001039703 No chr1 16788047 16788336-4.5 No 3, 50KDA 363 LOC51136 PTD016 PROTEIN NM_016125 No chr17 55396335 55396518-4.5 No chr17 55400431 55400634-4.4 No 364 MOV10 MOV10, MOLONEY LEUKEMIA VIRUS 10, HOMOLOG (MOUSE) NM_020963 No chr1 113017954 113018169 + 4.5 3.3 No 365 PRICKLE2 PRICKLE-LIKE 2 (DROSOPHILA) NM_198859 No chr3 64185454 64185746-4.5 No 366 PARN POLY(A)-SPECIFIC RIBONUCLEASE (DEADENYLATION NM_002582 No chr16 14632616 14632794-4.4 3.1 No NUCLEASE) 367 FLJ42953 FLJ42953 PROTEIN NM_207474 No chr22 19817117 19817362 + 4.4 No 368 C11ORF71 HYPOTHETICAL PROTEIN FLJ20010 NM_019021 No chr11 113775580 113775722-4.4 2.6 No 369 LAT LINKER FOR ACTIVATION OF T CELLS NM_001014987 No chr16 28994201 28994339 + 4.4 2.9 No 370 VIM VIMENTIN NM_003380 No chr10 17312619 17312794 + 4.4 4.1 No 371 CRIPAK HYPOTHETICAL PROTEIN FLJ34443 NM_175918 Yes chr4 1381391 1381551 + 4.4 2.5 No chr4 1381973 1382179 + 4.3 No 372 LOC441251 SIMILAR TO WILLIAMS BEUREN SYNDROME CHROMOSOME NM_001034844 No chr7 71975219 71975415-4.4 No REGION 19 373 PPAT PHOSPHORIBOSYL PYROPHOSPHATE AMIDOTRANSFERASE NM_002703 No chr4 56995417 56995655-4.4 No 374 KNDC1 KINASE NON-CATALYTIC C-LOBE DOMAIN (KIND) NM_152643 No chr10 134819329 134819607 + 4.4 No CONTAINING 1 375 THOC7 NGG1 INTERACTING FACTOR 3 LIKE 1 BINDING PROTEIN 1 NM_025075 No chr3 63823207 63823432-4.4 No 376 COX11 COX11 HOMOLOG, CYTOCHROME C OXIDASE ASSEMBLY NM_004375 No chr17 50399070 50399213-4.4 3.3 No PROTEIN (YEAST) 377 DAPL1 SIMILAR TO DEATH-ASSOCIATED PROTEIN NM_001017920 No chr2 159440389 159440616 + 4.4 No 378 SERF1A SMALL EDRK-RICH FACTOR 1A (TELOMERIC) NM_021967 No chr5 70122616 70122758 + 4.4 No 379 C3ORF10 CHROMOSOME 3 OPEN READING FRAME 10 NM_018462 No chr3 10131959 10132257 + 4.4 3.2 Yes 10132144, 10132166, 10132245 380 SQLE SQUALENE EPOXIDASE NM_003129 No chr8 126080239 126080438 + 4.4 3.2 Yes 126080360 381 NA NA NM_006955 Yes chr10 42095583 42095950-4.3 3.1 No 382 TUBB8 TUBULIN, BETA 8 NM_177987 No chr10 124852 125004-4.3 3.0 No 383 C6ORF126 AAAL3045 NM_207409 No chr6 35850972 35851148 + 4.3 4.3 No 384 PILRB PAIRED IMMUNOGLOBIN-LIKE TYPE 2 RECEPTOR BETA NM_175047 No chr7 99774960 99775088 + 4.3 3.2 No 385 CCDC107 HYPOTHETICAL PROTEIN MGC31967 NM_174923 No chr9 35646817 35646998 + 4.3 No 386 OR4F17 OLFACTORY RECEPTOR, FAMILY 4, SUBFAMILY F, MEMBER NM_001005240 No chr19 19675 19815 + 4.3 No 17 387 WSB1 WD REPEAT AND SOCS BOX-CONTAINING 1 NM_015626 Yes chr17 22644839 22645013 + 4.3 2.8 No 388 CASR CALCIUM-SENSING RECEPTOR (HYPOCALCIURIC NM_000388 No chr3 123378426 123378591 + 4.2 3.3 No HYPERCALCEMIA 1, SEVERE NEONATAL HYPERPARATHYROIDISM) 389 OR2V2 OLFACTORY RECEPTOR, FAMILY 2, SUBFAMILY V, MEMBER 2 NM_206880 No chr5 180462185 180462392 + 4.2 4.7 No 390 PTPRG PROTEIN TYROSINE PHOSPHATASE, RECEPTOR TYPE, G NM_002841 No chr3 61707267 61707515 + 4.1 Yes 61707486 391 RGS20 REGULATOR OF G-PROTEIN SIGNALLING 20 NM_003702 No chr8 54950054 54950234 + 4.1 2.7 No 392 CDH26 CADHERIN-LIKE 26 NM_021810 No chr20 57998013 57998193 + 4.1 Yes 57998025 393 FAM129B CHROMOSOME 9 OPEN READING FRAME 88 NM_001035534 No chr9 129381976 129382127-4.0 4.8 No 394 CHMP2B CHROMATIN MODIFYING PROTEIN 2B NM_014043 No chr3 87356241 87356416 + 4.0 No Supplemental material Page 13

Genome-wide analysis of HIF DNA-bdg-supplemental material Table S3. Sequences immunoprecipitatg with anti-α The table gives the chromosomal co-ordates of each anti-α immunoprecipitated locus meetg criteria of an MA Z of > 4, a width of > 100bp or > 5 probes, and a false discovery rate of < 5%, together with the maximum Z anti-α and anti-α at that gene locus. The presence or absence, and position of any HRE core motif with these sequences is given. The table also specifies whether the nearest gene to the immunoprecipitated locus was significantly regulated by exposure of cells to 1% hypoxia or 2mM DMOG or by transfection of sirnas directed agast α, α or both sirnas the Affymetrix s. Note that at a of loci several sequences were immunoprecipitated that shared proximity to a common transcriptional start site. These loci are listed order with the most strongly enriched site dicated black type and others grey type. Name chromosome start end strand Coordates of 1 ASMT ACETYLSEROTONIN O-METHYLTRANSFERASE NM_004043 No chrx 1842483 1844249 + 21.9 17.9 Yes 1844029, 1844146 2 PLS3 PLASTIN 3 (T ISOFORM) NM_005032 No chrx 114898432 114899202 + 17.4 15.8 Yes 114898465, 114898462, 114898505, 114898572, 114898984, 114899078, 114899133, 114899130 3 ZMYND8 PROTEIN KINASE C BINDING PROTEIN 1 NM_012408 Yes chr20 45422559 45423470-15.2 12.1 Yes 45422676 chr20 45421078 45421975-12.5 Yes 45421140, 45421318 4 FAM139A HYPOTHETICAL PROTEIN FLJ40722 NM_173678 Yes chr7 143028228 143029153 + 14.0 11.8 Yes 143028431, 143028490 5 TF TRANSFERRIN NM_001063 No chr3 134944026 134944856 + 13.6 10.7 Yes 134944391 6 DHX35 DEAH (ASP-GLU-ALA-HIS) BOX POLYPEPTIDE 35 NM_021931 No chr20 37022195 37022900 + 12.7 5.6 No 7 SEC61G SEC61 GAMMA SUBUNIT NM_001012456 No chr7 54794671 54794993-12.2 13.4 No 8 HIG2 HYPOXIA-INDUCIBLE PROTEIN 2 NM_013332 Yes chr7 127882554 127883114 + 12.1 9.5 Yes 127882971, 127883052, 127883064, 127883083, 127883101 9 CITED2 CBP/P300-INTERACTING TRANSACTIVATOR, WITH GLU/ASP-RICH CARBOXY-TERMINAL DOMAIN, 2 10 RAPGEF1 RAP GUANINE NUCLEOTIDE EXCHANGE FACTOR (GEF) 1 11 CHD1L CHROMODOMAIN HELICASE DNA BINDING PROTEIN 1-LIKE NM_006079 Yes chr6 139738163 139739480-12.1 8.1 Yes 139738268, 139738573, 139738619, 139738629, 139738646 NM_005312 No chr9 133609690 133610065-12.0 6.2 Yes 133609802, 133609799, 133609921 NM_004284 No chr1 145181416 145181919 + 11.9 7.5 Yes 145181605, 145181698, 145181738 12 UPK1B UROPLAKIN 1B NM_006952 No chr3 120386306 120387057 + 11.7 8.6 Yes 120386572 13 KIAA0195 KIAA0195 NM_014738 No chr17 70960840 70961202 + 11.6 9.7 Yes 70960909 14 BACE2 BETA-SITE APP-CLEAVING ENZYME 2 NM_138992 Yes chr21 41458829 41460026 + 11.4 8.7 Yes 41459310, 41459982 15 C1ORF161 CHROMOSOME 1 OPEN READING FRAME 161 NM_152367 No chr1 116455368 116456452 + 11.2 6.9 Yes 116455489, 116455851 16 GPRC5A G PROTEIN-COUPLED RECEPTOR, FAMILY C, NM_003979 Yes chr12 12916200 12917123 + 11.2 6.1 Yes 12916634 GROUP 5, MEMBER A 17 UBC UBIQUITIN C NM_021009 No chr12 123966902 123967854-11.2 7.4 No 18 S100A4 S100 CALCIUM BINDING PROTEIN A4 (CALCIUM PROTEIN, CALVASCULIN, METASTASIN, MURINE PLACENTAL HOMOLOG) NM_002961 Yes chr1 151784245 151784831-11.1 4.7 Yes 151784430, 151784576, 151784589, 151784676, 151784710 19 FLJ16641 FLJ16641 PROTEIN NM_001004316 No chr3 158017688 158018251 + 10.8 9.3 Yes 158017699, Supplemental material Page 14