Sample overview
| Species: | Human |
| Biosample type: | Cell line |
| Tissue type: | Colon |
| Data source: | NCBI GEO/SRA |
| Biosample name: | HCT116 TP53-/-_Nutlin3A |
| Sample ID: | Sample_02_0598 |
| SE ID | SE Region | Size | Rank | Element | Common SNP | eQTL | Risk SNP | TFBS | CRISPR Cas9 | Gene |
|---|---|---|---|---|---|---|---|---|---|---|
| SE_02_059800016 | chr1:84144189-84178300 |
34111 | 16 | 12 | 697 | 16 | 1 | 45 | 126 | PRKACB |
| SE_02_059800018 | chr10:112514860-112539964 |
25104 | 18 | 13 | 561 | 3 | 1 | 302 | 102 | VTI1A |
| SE_02_059800024 | chr10:28090128-28139980 |
49852 | 24 | 23 | 1317 | 69 | 8 | 73 | 222 | MPP7,ARMC4 |
| SE_02_059800011 | chr11:122136764-122200466 |
63702 | 11 | 38 | 1708 | 37 | 6 | 336 | 156 | MIR100,MIRLET7A2,MIR100HG,MIR125B1,BLID |
| SE_02_059800025 | chr12:37235267-37266848 |
31581 | 25 | 22 | 0 | 10 | 0 | 0 | 0 | |
| SE_02_059800046 | chr12:65630741-65657855 |
27114 | 46 | 9 | 738 | 28 | 0 | 111 | 0 | LOC100507065 |
| SE_02_059800045 | chr12:75622396-75643126 |
20730 | 45 | 14 | 578 | 95 | 3 | 46 | 0 | KRR1 |
| SE_02_059800020 | chr12:75697411-75751536 |
54125 | 20 | 28 | 1543 | 48 | 4 | 95 | 0 | KRR1 |
| SE_02_059800014 | chr12:88920286-88962244 |
41958 | 14 | 25 | 938 | 25 | 3 | 165 | 0 | LOC728084 |
| SE_02_059800021 | chr15:19775273-19789856 |
14583 | 21 | 9 | 0 | 6 | 0 | 0 | 0 | CHEK2P2 |
| SE_02_059800028 | chr16:38265908-38280538 |
14630 | 28 | 9 | 0 | 0 | 0 | 0 | 0 | |
| SE_02_059800030 | chr17:59828001-59847227 |
19226 | 30 | 13 | 424 | 30 | 0 | 88 | 204 | MIR21,VMP1,RPS6KB1,TUBD1 |
| SE_02_059800033 | chr18:3595778-3626471 |
30693 | 33 | 10 | 809 | 47 | 3 | 47 | 658 | DLGAP1,DLGAP1-AS2,DLGAP1-AS1 |
| SE_02_059800041 | chr2:181777223-181792720 |
15497 | 41 | 9 | 392 | 8 | 0 | 70 | 0 | NEUROD1,SSFA2 |
| SE_02_059800029 | chr2:226114102-226138394 |
24292 | 29 | 9 | 666 | 15 | 3 | 73 | 0 | LOC646736 |
| SE_02_059800034 | chr2:226151410-226191808 |
40398 | 34 | 16 | 1033 | 72 | 4 | 118 | 216 | LOC646736 |
| SE_02_059800035 | chr2:226649432-226674907 |
25475 | 35 | 13 | 703 | 4 | 0 | 110 | 48 | MIR5702 |
| SE_02_059800022 | chr20:28494677-28498118 |
3441 | 22 | 5 | 0 | 1 | 0 | 0 | 0 | FRG1CP |
| SE_02_059800027 | chr3:111902234-111937367 |
35133 | 27 | 19 | 920 | 88 | 4 | 95 | 606 | PHLDB2,ABHD10 |
| SE_02_059800044 | chr3:91543633-91553282 |
9649 | 44 | 6 | 0 | 0 | 0 | 0 | 0 | |
| SE_02_059800038 | chr3:93705594-93722456 |
16862 | 38 | 10 | 0 | 9 | 0 | 0 | 0 | PROS1 |
| SE_02_059800032 | chr3:98536047-98565438 |
29391 | 32 | 14 | 756 | 55 | 2 | 77 | 0 | OR5K2,GPR15,CLDND1,CPOX |
| SE_02_059800026 | chr3:98955284-98985980 |
30696 | 26 | 20 | 739 | 105 | 0 | 66 | 0 | DCBLD2 |
| SE_02_059800010 | chr4:101101377-101165282 |
63905 | 10 | 36 | 1603 | 56 | 7 | 166 | 31 | PPP3CA,MIR8066 |
| SE_02_059800003 | chr4:30743156-30877760 |
134604 | 3 | 78 | 3710 | 87 | 7 | 752 | 0 | PCDH7 |
| SE_02_059800009 | chr4:30900946-30963773 |
62827 | 9 | 36 | 1760 | 87 | 4 | 256 | 45 | PCDH7 |
| SE_02_059800017 | chr4:31018245-31069446 |
51201 | 17 | 29 | 1545 | 0 | 4 | 182 | 0 | PCDH7,LOC102723778 |
| SE_02_059800002 | chr4:49708186-49711944 |
3758 | 2 | 4 | 0 | 0 | 0 | 0 | 0 | CWH43,OCIAD2 |
| SE_02_059800015 | chr4:74620343-74671187 |
50844 | 15 | 39 | 1522 | 13 | 3 | 68 | 0 | BTC |
| SE_02_059800007 | chr5:49609746-49646309 |
36563 | 7 | 34 | 0 | 2 | 0 | 0 | 0 | EMB |
| SE_02_059800023 | chr7:130886789-130917926 |
31137 | 23 | 25 | 977 | 59 | 4 | 101 | 118 | LOC100506860,LINC-PINT,MIR29A,MIR29B1 |
| SE_02_059800039 | chr7:130994408-131016195 |
21787 | 39 | 17 | 547 | 21 | 3 | 64 | 62 | LINC-PINT,LOC100506860 |
| SE_02_059800031 | chr8:127206659-127225802 |
19143 | 31 | 10 | 538 | 4 | 1 | 104 | 360 | CCAT1,CASC21,CASC19 |
| SE_02_059800012 | chr8:43237596-43242014 |
4418 | 12 | 5 | 264 | 10 | 0 | 0 | 0 | POTEA,HGSNAT |
| SE_02_059800040 | chr8:93837193-93858651 |
21458 | 40 | 8 | 591 | 35 | 0 | 58 | 0 | MIR378D2 |
| SE_02_059800043 | chr8:93872356-93884936 |
12580 | 43 | 12 | 361 | 10 | 3 | 15 | 0 | PDP1,MIR378D2 |
| SE_02_059800036 | chr8:93897585-93921315 |
23730 | 36 | 12 | 648 | 36 | 1 | 130 | 377 | PDP1,MIR378D2 |
| SE_02_059800013 | chr9:21553173-21593941 |
40768 | 13 | 24 | 1145 | 15 | 7 | 97 | 166 | MIR31HG,MIR31 |
| SE_02_059800019 | chr9:21668852-21692880 |
24028 | 19 | 13 | 929 | 50 | 11 | 70 | 0 | MIR31HG |
| SE_02_059800005 | chr9:60552679-60688438 |
135759 | 5 | 65 | 0 | 0 | 0 | 0 | 0 | SPATA31A5 |
| SE_02_059800006 | chrUn_KI270333v1:4-2696 |
2692 | 6 | 3 | 0 | 0 | 0 | 0 | 0 | |
| SE_02_059800037 | chrUn_KI270336v1:14-1025 |
1011 | 37 | 1 | 0 | 0 | 0 | 0 | 0 | |
| SE_02_059800008 | chrUn_KI270337v1:12-1087 |
1075 | 8 | 1 | 0 | 0 | 0 | 0 | 0 | |
| SE_02_059800042 | chrUn_KI270411v1:115-2452 |
2337 | 42 | 4 | 0 | 0 | 0 | 0 | 0 | |
| SE_02_059800004 | chrUn_KI270466v1:2-1208 |
1206 | 4 | 1 | 0 | 0 | 0 | 0 | 0 | |
| SE_02_059800001 | chrUn_KI270467v1:852-3889 |
3037 | 1 | 4 | 0 | 0 | 0 | 0 | 0 |
SE annotation visualization
Information description of sample and annotation
| Case ID: | Name:GSM3020150 |
| Input ID: | Name:GSM3020144 |
| Common SNP: | dbSNP |
| eQTL: | GTEx, HaploReg v4.1, PancanQTL |
| Risk SNP : | GWAS Catalog, GWASdb v2.0 |
| TFBS: | TFBS Conserved of UCSC |
| CRISPR/Cas9 target site: | CRISPR Targets of UCSC |
Software and parameters used
| Read Mapping: | bowtie(v2.4.4) -p 10 -x -S -U |
| Peak Calling: | macs2 callpeak -t -c -f BAM -B -g hs(mm) -q 0.01 --keep-dup=auto |
| Stitching Distance: | 12.5 kb |
| TSS Exclusive Zone: | +/- 2 kb |