rearrangement_ID path_to_processed_hic_data rearrangement_type cell_type capture_WT_raw_data capture_Mut_raw_data cite genome_assembly chr start_capture end_capture start1 end1 start2 end2 start3 end3 start4 end4 start5 end5 start6 end6 comments path_to_processed_CTCF_data CTCF_raw_data CTCF_input Kit30 ./hic_data/deletion/Kit30/ deletion mast_cell mm10 chr5 74130000 76415000 75852780 75881218 ./CTCF_data/mast_cells our data our data Kit30plus ./hic_data/deletion/Kit30plus/ deletion mast_cell mm10 chr5 74130000 76415000 75736367 757336679 75852780 75881218 ./CTCF_data/mast_cells our data our data MusDelB ./hic_data/deletion/MusDelB/ deletion E11.5 distal limb buds SRR5099908 SRR5099909 "Bianco Simona et al. ""Polymer physics predicts the effects of structural variants on chromatin architecture."" Nature genetics 50.5 (2018): 662-667." mm10 chr1 70945000 81010000 76395828 78067689 ./CTCF_data/SRX1975285-SRX1975286 SRX1975285-SRX1975286 SRX4096939 DelB ./hic_data/deletion/DelB/ deletion human fibroblasts SRX2416656 SRX2416657 "Bianco Simona et al. ""Polymer physics predicts the effects of structural variants on chromatin architecture."" Nature genetics 50.5 (2018): 662-667." hg38 chr2 217445000 223235000 220413511 222149613 ./CTCF_data/SRX1975285-SRX1975286 SRX1975285-SRX1975286 SRX4096940 Bor ./hic_data/deletion/Bor/ deletion E12.5 limb buds SRX1593831 SRX1593833 "Franke Martin et al. ""Formation of new chromatin domains determines pathogenicity of genomic duplications."" Nature 538.7624 (2016): 265-269." mm10 chr11 109140001 115015000 111522545 111540886 ./CTCF_data/SRX5259427-SRX5259428 SRX5259427-SRX5259428 SRX4096941 DelL-Mm ./hic_data/deletion/DelL-Mm/ deletion Forelimb E11.5 "SRX3175632; SRX3175633; SRX3175634; SRX3175635" SRX3175656-SRX3175657 "Kragesteen Bjƒñrt K. et al. ""Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis."" Nature genetics 50.10 (2018): 1463-1473." mm10 chr13 53895001 57200000 56048376 56147390 ./CTCF_data/SRX1975279 SRX1975279 SRX4096942 Neur1-Mm ./hic_data/deletion/Neur1-Mm/ deletion Forelimb E11.5 "SRX3175632; SRX3175633; SRX3175634; SRX3175635" SRX3175662-SRX3175663 "Kragesteen Bjƒñrt K. et al. ""Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis."" Nature genetics 50.10 (2018): 1463-1473." mm10 chr13 53895001 57200000 56219601 56264136 ./CTCF_data/SRX1975279 SRX1975279 SRX4096943 ZRSreg ./hic_data/deletion/ZRSreg/ deletion FLHL "SRX5099269; SRX5099270; SRX5764173" "SRX5764174; " "Paliou Christina et al. ""Preformed chromatin topology assists transcriptional robustness of Shh during limb development."" Proceedings of the National Academy of Sciences 116.25 (2019): 12390-12399." mm10 chr5 27460000 30345000 29314818 29315227 "./CTCF_data/SRX5099280;SRX5099281" "SRX5099280;SRX5099281" SRX4096944 Lprom ./hic_data/deletion/Lprom/ deletion FLHL "SRX5099269; SRX5099270; SRX5764173" "SRX5099268; SRX5764172" "Paliou Christina et al. ""Preformed chromatin topology assists transcriptional robustness of Shh during limb development."" Proceedings of the National Academy of Sciences 116.25 (2019): 12390-12399." mm10 chr5 27460000 30345000 "./CTCF_data/SRX5099280;SRX5099281" "SRX5099280;SRX5099281" SRX4096945 FirreKO_1 ./hic_data/deletion/FirreKO_1/ deletion MEF female SRX3241571-SRX3241578 SRX3241579-SRX3241585 "Barutcu A. Rasim et al. ""A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus."" Nature communications 9.1 (2018): 1-11." mm10 chrX 50550000 50675000 50555286 50637116 ./CTCF_data/SRX3230671-SRX3230678 SRX3230671-SRX3230678 SRX3230694-SRX3230695 FirreKO_2 ./hic_data/deletion/FirreKO_2/ deletion MEF male SRX3241586-SRX3241589 SRX3241590-SRX3241595 "Barutcu A. Rasim et al. ""A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus."" Nature communications 9.1 (2018): 1-11." mm10 chrX 50550000 50675000 50555286 50637116 ./CTCF_data/SRX3230671-SRX3230678 SRX3230671-SRX3230678 SRX4096947 FirreKO_3 ./hic_data/deletion/FirreKO_3/ deletion mESC male SRX3269798-SRX3269799 SRX3269796-SRX3269797 "Barutcu A. Rasim et al. ""A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus."" Nature communications 9.1 (2018): 1-11." mm10 chrX 50550000 50675000 50555286 50637116 ./CTCF_data/SRX3230671-SRX3230678 SRX3230671-SRX3230678 SRX4096948 del1-13d9lac_1 ./hic_data/deletion/del1-13d9lac_1/ deletion_2 Distal Forelimb E12 SRX3024410 SRX3024412 "Rodrƒ?guez-Carballo Eddie et al. ""The HoxD cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes."" Genes & development 31.22 (2017): 2264-2281." mm10 chr2 70945000 81015000 74663890 74693921 74701834 74764314 ./CTCF_data/SRX3024492 SRX3024492 SRX4096949 del1-13d9lac_2 ./hic_data/deletion/del1-13d9lac_2/ deletion_2 Proximal Forelimb E12 SRX3024415 SRX3024413 "Rodrƒ?guez-Carballo Eddie et al. ""The HoxD cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes."" Genes & development 31.22 (2017): 2264-2281." mm10 chr2 70945000 81015000 74663890 74693921 74701834 74764314 ./CTCF_data/SRX3024493 SRX3024493 SRX4096950 delattP-Rel5d9lac_1 ./hic_data/deletion/delattP-Rel5d9lac_1/ deletion_2 Distal Forelimb E12 SRX3024410 SRX3024414 "Rodrƒ?guez-Carballo Eddie et al. ""The HoxD cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes."" Genes & development 31.22 (2017): 2264-2281." mm10 chr2 70945000 81015000 74422050 74693922 74701834 7468746 ./CTCF_data/SRX3024492 SRX3024492 SRX4096951 delattP-Rel5d9lac_2 ./hic_data/deletion/delattP-Rel5d9lac_2/ deletion_2 Proximal Forelimb E12 SRX3024415 SRX3024415 "Rodrƒ?guez-Carballo Eddie et al. ""The HoxD cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes."" Genes & development 31.22 (2017): 2264-2281." mm10 chr2 70945000 81015000 74422050 74693922 74701834 7468746 ./CTCF_data/SRX3024493 SRX3024493 SRX4096952 BorC1 ./hic_data/deletion/BorC1/ deletion_2 E12.5 limb buds SRX1593831 SRX5260103 "Franke Martin et al. ""Formation of new chromatin domains determines pathogenicity of genomic duplications."" Nature 538.7624 (2016): 265-269." mm10 chr11 109140001 115015000 111904229 111904329 111522535 111540879 ./CTCF_data/SRX5259427-SRX5259428 SRX5259427-SRX5259428 SRX4096953 D3839 ./hic_data/deletion/D3839/ deletion_2 erythroid cells "SRX2741786-SRX2741788; SRX2741771-SRX2741773; SRX2741762-SRX2741764" "SRX2741789-SRX2741791; " "Kragesteen Bjƒñrt K. et al. ""Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis."" Nature genetics 50.10 (2018): 1463-1473." mm10 chr11 32190000 32335000 32238646 32238667 32237202 32237228 - i4i5 ./hic_data/deletion/i4i5/ deletion_2 FLHL "SRX5099269; SRX5099270; SRX5764173" "SRX5099264; SRX5099265" "Paliou Christina et al. ""Preformed chromatin topology assists transcriptional robustness of Shh during limb development."" Proceedings of the National Academy of Sciences 116.25 (2019): 12390-12399." mm10 chr5 27465001 30345000 29293392 29293421 29336029 29336056 "./CTCF_data/SRX5099280;SRX5099281" "SRX5099280;SRX5099281" SRX4096949 BorC1-2 ./hic_data/deletion/BorC1-2/ deletion_3 E12.5 limb buds SRX1593831 SRX5260104 "Franke Martin et al. ""Formation of new chromatin domains determines pathogenicity of genomic duplications."" Nature 538.7624 (2016): 265-269." mm10 chr11 109140001 115015000 112209542 112209642 111522535 111540879 111653006 111653106 ./CTCF_data/SRX5259427-SRX5259428 SRX5259427-SRX5259428 SRX4096950 i4i5ZRSreg ./hic_data/deletion/i4i5ZRSreg/ deletion_3 FLHL "SRX5099269; SRX5099270; SRX5764173" "SRX5764177; SRX5764178" "Paliou Christina et al. ""Preformed chromatin topology assists transcriptional robustness of Shh during limb development."" Proceedings of the National Academy of Sciences 116.25 (2019): 12390-12399." mm10 chr5 27460000 30345000 29293392 29293421 29336029 29336056 29314818 29315227 "./CTCF_data/SRX5099280;SRX5099281" "SRX5099280;SRX5099281" SRX4096951 i4i5ZRS_1 ./hic_data/deletion/i4i5ZRS_1/ deletion_3 FLHL "SRX5099269; SRX5099270; SRX5764173" "SRX5099266; SRX5099267" "Paliou Christina et al. ""Preformed chromatin topology assists transcriptional robustness of Shh during limb development."" Proceedings of the National Academy of Sciences 116.25 (2019): 12390-12399." mm10 chr5 27460000 30345000 29293392 29293421 29336029 29336056 29314814 29314832 "./CTCF_data/SRX5099280;SRX5099281" "SRX5099280;SRX5099281" SRX4096952 i4i5ZRS_2 ./hic_data/deletion/i4i5ZRS_2/ deletion_3 midbrain "SRX5099272; SRX5099273" "SRX5764175; SRX5764176" "Paliou Christina et al. ""Preformed chromatin topology assists transcriptional robustness of Shh during limb development."" Proceedings of the National Academy of Sciences 116.25 (2019): 12390-12399." mm10 chr5 27460000 30345000 29293392 29293421 29336029 29336056 29314814 29314832 "./CTCF_data/SRX5099280;SRX5099281" "SRX5099280;SRX5099281" SRX4096953 BorC1-4 ./hic_data/deletion/BorC1-4/ deletion_5 E12.5 limb buds SRX1593831 SRX5260105 "Franke Martin et al. ""Formation of new chromatin domains determines pathogenicity of genomic duplications."" Nature 538.7624 (2016): 265-269." mm10 chr11 109140001 115015000 111522535 111540879 111514320 111653006 111653106 111904229 111904329 111964807 112103393 112103493 ./CTCF_data/SRX5259427-SRX5259428 SRX5259427-SRX5259428 SRX4096954 dup-S ./hic_data/duplication/dup-S/ duplication E12.5 limb buds SRX1593831 SRX1889696 "Franke Martin et al. ""Formation of new chromatin domains determines pathogenicity of genomic duplications."" Nature 538.7624 (2016): 265-269." mm10 chr11 109140001 115015000 111891303 112311622 ./CTCF_data/SRX5259427-SRX5259428 SRX5259427-SRX5259428 SRX4096955 dup-L ./hic_data/duplication/dup-L/ duplication E12.5 limb buds SRX1593831 SRX1593832 "Franke Martin et al. ""Formation of new chromatin domains determines pathogenicity of genomic duplications."" Nature 538.7624 (2016): 265-269." mm10 chr11 109140001 115015000 111098275 112653378 ./CTCF_data/SRX5259427-SRX5259428 SRX5259427-SRX5259428 SRX4096956 dup-C ./hic_data/duplication/dup-C/ duplication E12.5 limb buds SRX1593831 SRX1889695 "Franke Martin et al. ""Formation of new chromatin domains determines pathogenicity of genomic duplications."" Nature 538.7624 (2016): 265-269." mm10 chr11 109140001 115015000 110910796 112653378 ./CTCF_data/SRX5259427-SRX5259428 SRX5259427-SRX5259428 SRX4096957 Dup-LBor ./hic_data/duplication_deletion/Dup-LBor/ duplication_deletion E12.5 limb buds SRX1593831 SRX1593834 "Franke Martin et al. ""Formation of new chromatin domains determines pathogenicity of genomic duplications."" Nature 538.7624 (2016): 265-269." mm10 chr11 109140001 115015000 111098275 112653378 111522545 111540886 ./CTCF_data/SRX5259427-SRX5259428 SRX5259427-SRX5259428 SRX4096958 InvF ./hic_data/inversion/InvF/ inversion E11.5 distal limb buds SRR5099908 SRR5099911 "Bianco Simona et al. ""Polymer physics predicts the effects of structural variants on chromatin architecture."" Nature genetics 50.5 (2018): 662-667." mm10 chr1 70945000 81010000 74786262 75902132 ./CTCF_data/SRX1975285-SRX1975286 SRX1975285-SRX1975286 SRX4096959 Inv1 ./hic_data/inversion/Inv1/ inversion forelimb E11.5 SRX4369709 SRX4369710 "Kraft Katerina et al. ""Serial genomic inversions induce tissue-specific architectural stripes gene misexpression and congenital malformations."" Nature cell biology 21.3 (2019): 305-310." mm10 chr1 70945000 81015000 75279391 75902131 ./CTCF_data/SRX1975279 SRX1975279 SRX4096960 Inv2 ./hic_data/inversion/Inv2/ inversion forelimb E11.5 SRX4369709 SRX4369711 "Kraft Katerina et al. ""Serial genomic inversions induce tissue-specific architectural stripes gene misexpression and congenital malformations."" Nature cell biology 21.3 (2019): 305-310." mm10 chr1 70945000 81015000 75135035 75902131 ./CTCF_data/SRX1975279 SRX1975279 SRX4096961 Inv3 ./hic_data/inversion/Inv3/ inversion forelimb E11.5 SRX4369709 SRX4369712 "Kraft Katerina et al. ""Serial genomic inversions induce tissue-specific architectural stripes gene misexpression and congenital malformations."" Nature cell biology 21.3 (2019): 305-310." mm10 chr1 70945000 81015000 74887741 75902131 ./CTCF_data/SRX1975279 SRX1975279 SRX4096962 Inv4 ./hic_data/inversion/Inv4/ inversion forelimb E11.5 SRX4369709 SRX4369713 "Kraft Katerina et al. ""Serial genomic inversions induce tissue-specific architectural stripes gene misexpression and congenital malformations."" Nature cell biology 21.3 (2019): 305-310." mm10 chr1 70945000 81015000 7489655 78902131 ./CTCF_data/SRX1975279 SRX1975279 SRX4096963 Inv1d ./hic_data/inversion/Inv1d/ inversion forelimb E11.5 SRX4369709 SRX4369714 "Kraft Katerina et al. ""Serial genomic inversions induce tissue-specific architectural stripes gene misexpression and congenital malformations."" Nature cell biology 21.3 (2019): 305-310." mm10 chr1 70945000 81015000 75650966 75655176 ./CTCF_data/SRX1975279 SRX1975279 SRX4096964 InvC ./hic_data/inversion/InvC/ inversion E12.5 limb buds SRX1593831 SRX5260108 "Franke Martin et al. ""Formation of new chromatin domains determines pathogenicity of genomic duplications."" Nature 538.7624 (2016): 265-269." mm10 chr11 109140001 115015000 111522535 112653434 ./CTCF_data/SRX5259427-SRX5259428 SRX5259427-SRX5259428 SRX4096965 InvIntra ./hic_data/inversion/InvIntra/ inversion E12.5 limb buds SRX1593831 SRX5260109 "Franke Martin et al. ""Formation of new chromatin domains determines pathogenicity of genomic duplications."" Nature 538.7624 (2016): 265-269." mm10 chr11 109140001 115015000 111540879 112653434 ./CTCF_data/SRX5259427-SRX5259428 SRX5259427-SRX5259428 SRX4096966 Inv1-Mm_1 ./hic_data/inversion/Inv1-Mm_1/ inversion Hindlimb E11.5 "SRX3175636; SRX3175637; SRX3175638; SRX3175639;" "SRX3542185; SRX4112993" "Kragesteen Bjƒñrt K. et al. ""Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis."" Nature genetics 50.10 (2018): 1463-1473." mm10 chr13 53895001 57200000 56048376 56160753 ./CTCF_data/SRX1975285-SRX1975286 SRX1975285-SRX1975286 SRX4096967 Inv1-Mm_2 ./hic_data/inversion/Inv1-Mm_2/ inversion Forelimb E11.5 "SRX3175632; SRX3175633; SRX3175634; SRX3175635" SRX3175654-SRX3175655 "Kragesteen Bjƒñrt K. et al. ""Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis."" Nature genetics 50.10 (2018): 1463-1473." mm10 chr13 53895001 57200000 56048376 56160753 ./CTCF_data/SRX1975285-SRX1975286 SRX1975285-SRX1975286 SRX4096968