Skip to main content

Table 1 Comparison of open chromatin features to single copy genomic regions with and without DA

From: Localized, non-random differences in chromatin accessibility between homologous metaphase chromosomes

   Open chromatin features
SC probe probe location [GRCh37] Gene interval or cytoband DNase-OS FAIR-OS H3K4me H3K9Ac H3K27Ac H3K4me2
chr1:1171789-1175143* 1p36.3, intergenic 11592 8710 544.0 168.4 115.6 120.6
chr1:1181574-1185503 FAM132A:Ex1-IVS1 7394 9695 596.5 143.0 102.8 160.9
chr1:1628792-1633615 CDK11B:IVS6 10378 14274 326.3 222.1 121.8 177.6
chr1:1632683-1637407 CDK11B:IVS6 12139 12829 290.7 125.8 51.8 51.8
chr1:240965538-240967390 RGS7:IVS13-IVS14 1420 9976 200.6 74.0 12.1 29.6
chr1:240988582-240990678* RGS7:IVS4-IVS5 2840 8999 125.3 55.3 7.4 59.2
chr4:3242502-3246008 HTT:Ex67 9225 15222 248.0 142.8 81.4 51.8
chr5:1421588-1425427 SLC6A3:IVS4-IVS5 4702 8574 172.0 80.3 66.6 14.8
chr5:9355970-9358454 SEMA5A:IVS3 2827 16953 235.4 103.6 36.5 29.6
chr5:9361501-9365307 SEMA5A:IVS3 12398 40009 3017.6 597.4 1993.0 1530.2
chr5:9371425-9374496 SEMA5A:IVS3 1397 18058 531.5 48.5 81.4 59.2
chr5:11042187-11044508 CTNND2:IVS16 2221 15462 253.7 80.3 32.6 44.4
chr5:11071700-11076039 CTNND2:IVS16 4422 19382 344.8 158.4 118.5 77.8
chr5:11084988-11089067 CTNND2:IVS15 2942 16403 297.3 81.4 81.4 22.2
chr5:68462247-68464721* CCNB1:Ex1-IVS3 31707 29162 1400.2 2378.9 1953.4 2076.3
chr7:73506616-73509661 L1MK1:IVS14 32349 30750 3473.0 4213.1 5870.8 4186.7
chr7:73534615-73536880 L1MK1:Ex1-IVS3 3639 9068 237.2 47.3 0 22.2
chr8:116658428-116661455 TRPS1:IVS1 3738 15369 650.0 224.2 78.6 396.1
chr8:116661938-116665132 TRPS1:IVS1 2031 15754 316.0 112.2 59.2 57.9
chr9:213762-215844* C9orf66:Ex1 10945 15191 868.4 1550.5 503.2 1667.6
chr9:133587757-133589963 ABL1:Ex1b-IVS1b 32515 25514 616.8 3043.7 2278.6 1563.2
chr9:133616347-133618188 ABL1:IVS1b 1917 10733 341.9 83.6 42.0 71.1
chr9:133733132-133735051 ABL1:IVS3 2859 8103 188.8 50.9 74.2 37.0
chr9:133735369-133737639 ABL1:IVS3 2211 11425 259.7 62.8 56.1 95.6
chr9:133745513-133749828 ABL1:IVS4-IVS6 18884 37627 4959.4 477.6 982.4 998.7
chr9:133759487-133764440 ABL1:Ex11 7053 15356 322.9 174.4 142.9 74.0
chr9:140952206-140954439* CACNA1B:Ex29-IVS31 4956 8277 302.2 88.8 33.8 51.8
chr9:140969092-140971796 CACNA1B:IVS33-IVS34 4127 7686 151.2 69.2 44.4 37.0
chr11:133180187-133182699* OPCML:IVS1 2306 11280 202.1 77.4 37.0 133.8
chr12:11958559-11960434 ETV6:IVS2 2403 19900 2947.6 327.2 751.8 757.8
chr12:11992883-11994726 ETV6:IVS2 2257 16709 786.4 134.8 384.3 62.9
chr12:11992883-11995741 ETV6:IVS3 2988 23954 887.0 206.0 453.6 232.7
chr13:100626271-100630715 13q32.3, intergenic 11678 18628 216.6 76.2 65.8 23.2
chr13:100643221-100648153 13q32.3, intergenic 7452 25389 687.8 115.4 83.2 221.4
chr15:22690247-22693115 15q11.2, intergenic 1705 4996 347.0 85.2 47.4 29.6
chr15:22853681-22855541 TUBGCP5:IVS11-IVS13 1049 21106 132.0 75.4 96.9 22.2
chr15:23864038-23868139 15q11.2, intergenic 4260 17789 272.4 74.0 38.6 79.6
chr15:23883747-23886037 15q11.2, intergenic 1969 6908 84.0 76.3 10.5 29.6
chr15:23886989-23890525 MAGEL2:Promoter- 3′UTR 7602 12049 198.2 88.8 51.8 50.9
chr15:25016909-25018586 15q11.2, intergenic 1670 5764 216.6 38.2 48.1 111.5
chr15:25052358-25054037 15q11.2, intergenic 671 6051 83.8 51.9 7.4 0
chr15:25068481-25070727* SNRPN: Promoter:IVS1 1524 7291 149.1 74.4 19.3 22.2
chr15:25199392-25201602 SNRPN:IVS4 6799 10253 258.1 1391.0 937.3 486.3
chr15:25613407-25617676 UBE3A:IVS7-IVS8 2728 26796 3025.0 81.4 182.8 96.0
chr15:27117096-27119866* GABRA5:IVS3 5815 8082 140.0 40.8 37.0 29.6
chr15:28509526-28511337* HERC2:IVS12-IVS13 4580 10908 854.2 313.8 728.2 465.3
chr15:102388168-102389774 OR4F13P:IVS3-Ex5 950 8872 64.0 47.6 37.0 29.6
chr16:15013674-15017156 16p13.11, intergenic 814 984 248.3 51.8 62.2 53.0
chr16:16412325-16415807 PKD1P1:IVS2-IVS7 473 268 168.0 76.8 71.4 51.8
chr16:16452359-16455837 16p13.11, intergenic 418 670 98.7 54.1 65.2 44.4
chr16:16234893-16236784 ABCC1:IVS30-Ex31 4867 11513 451.2 103.6 89.3 45.6
chr16:18440574-18444056 16p12.3, intergenic 110 0 181.5 74.0 73.4 31.2
chr16:18484058-18487536 16p12.3, intergenic 616 907 167.7 89.9 51.8 19.1
chr17:905599-910582 ABR:IVS21-3′UTR 10824 19481 304.9 174.9 132.8 2.9
chr17:941273-943865 ABR:IVS16 3508 6315 170.9 89.1 74.0 71.8
chr17:2591614-2594572 CLUH:IVS25-3′UTR 10756 11515 576.5 96.2 384.9 163.2
chr17:2596810-2599164 CLUH:IVS13-IVS19 5323 6551 301.9 112.5 63.3 37.0
chr17:2603297-2606091 CLUH:IVS3-IVS9 7600 7093 222.1 57.0 51.8 123.2
chr17:18128679-18133300 LLGL1:Promoter-Ex2 36213 27618 1016.0 647.8 219.2 743.9
chr17:18143933-18146387 LLGL1:Ex17-IVS22 7467 8690 136.8 114.2 37.0 16.8
chr17:15133018-15136902* PMP22:IVS4-Ex5 5482 14180 207.3 113.3 60.8 34.6
chr17:15150757-15153084* PMP22:IVS3 4694 12616 321.0 77.7 28.7 44.4
chr17:15174803-15176657 17p12, intergenic 2574 11 163.0 89.3 37.0 31.4
chr17:15847751-15849832* ADORA2B:Promoter-Ex1 10751 9889 763.1 241.5 79.0 980.8
chr17:15868752-15870532* ADORA2B:IVS1 2859 17457 711.4 95.0 78.8 84.7
chr17:18150509-18152632 FLII:IVS15-Ex21 23767 14999 2289.9 74.7 439.4 75.6
chr17:18153505-18154823 FLII:IVS12-IVS14 3547 3937 47.1 36.7 36.8 0
chr17:19286892-19288934 MFAP4:IVS3-Ex6 3415 5897 286.5 139.3 95.8 54.8
chr17:37861465-37863632 ERBB2:IVS5-IVS6 5114 6170 296.6 90.6 78.3 84.4
chr17:37882684-37886219 ERBB2:IVS27-Ex31 9666 16440 1561.2 617.8 331.8 836.4
chr17:38500482-38504359 RARA:IVS2 17458 19211 3584.2 597.6 650.9 813.2
chr17:38512106-38514271 RARA: IVS8-Ex9 5468 6830 177.2 130.6 125.8 88.3
chr17:38608442-38610468 IGFBP4:IVS1-IVS3 4526 10512 230.8 39.5 29.6 62.7
chr17:38613433-38617530 IGFBP4:Ex4 8748 18085 557.1 155.4 88.8 74.0
chr17:80290070-80293112 SECTM1:Ex1-IVS1 13714 13008 2005.4 294.1 202.4 1002.5
chr20:10642756-10644909 JAG1:IVS2-IVS3 2943 15006 1104.1 118.6 49.2 225.7
chr21:36259933-36264124 RUNX1:IVS2 26119 30777 1920.4 2050.4 1478.7 2915.8
chr21:39454065-39456057 DSCR4:IVS2 2440 7032 155.4 65.3 24.6 65.9
chr21:39463783-39466136 DSCR4:IVS2 2017 10359 126.5 63.2 51.8 25.6
chr21:39473031-39475467 DSCR4:IVS2 2256 10103 137.4 86.9 37.0 0.2
chr22:19338598-19342289 HIRA:IVS21-IVS24 3429 12123 325.1 150.0 59.2 37.0
chr22:23578368-23581572 BCR:IVS1 6792 19899 2489.1 283.0 240.2 284.8
chr22:23604414-23607814 BCR:IVS4 11921 14381 1989.6 425.4 621.7 362.3
chr22:23623055-23625566 BCR:IVS8 21132 16241 2543.9 311.6 501.8 451.4
chr22:51175125-51178674* ACR:Ex1-IVS3 11986 12916 175.2 85.1 37.0 58.9
chrX:592626-595515 SHOX:IVS2-Ex3 7316 7254 125.9 55.3 29.6 37.0
chrX:597816-600430 SHOX:IVS3 6234 7821 64.0 74.0 41.5 44.4
chrX:602538-605057 SHOX:IVS5 4319 4191 147.9 29.6 7.0 14.8
chrX:7891853-7895877 PNPLA4:Ex1-IVS2 19932 42372 1854.3 2340.4 2553.7 1715.7
chrX:8440844-8443508 Xp22.31, intergenic 1639 12112 151.2 59.2 30.0 45.5
chrX:8505855-8509075 KAL1:IVS9-IVS10 4319 14875 147.9 106.6 14.8 44.4
chrX:9613498-9617784 TBL1X:IVS4 4522 20294 429.2 164.6 115.6 133.7
chrX:9685383-9689409 TBL1X:Ex18 3938 43044 336.8 101.4 65.5 90.3
  1. Probes from 93 genomic regions exhibiting DA (bold) or equivalent accessibility by metaphase FISH listed by chromosome number and GRCh37 genomic coordinates. Single copy intervals marked with * were characterized by FISH in this study; the other intervals were previously reported.20–25 Single copy probes that overlapped genes are specified relative to their exonic (Ex), intronic (IVS) or untranslated (UTR) positions. Single copy probes from intergenic regions were specified by cytogenetic location. Integrated signal intensities of the open chromatin features from ENCODE 27 are shown. As appropriate, values are shown with one significant digit after the decimal.