Sample overview
| Species: | Human |
| Biosample type: | Cell line |
| Tissue type: | Brain |
| Data source: | NCBI GEO/SRA |
| Biosample name: | Kelly_shLUC_Res |
| Sample ID: | Sample_02_0700 |
| SE ID | SE Region | Size | Rank | Element | Common SNP | eQTL | Risk SNP | TFBS | CRISPR Cas9 | Gene |
|---|---|---|---|---|---|---|---|---|---|---|
| SE_02_070000026 | chr1:116359304-116376214 |
16910 | 26 | 6 | 393 | 5 | 1 | 83 | 550 | ATP1A1,ATP1A1-AS1 |
| SE_02_070000033 | chr1:23554293-23581310 |
27017 | 33 | 6 | 777 | 47 | 1 | 199 | 382 | ID3,E2F2,LOC101928163,MDS2 |
| SE_02_070000029 | chr1:244046758-244057139 |
10381 | 29 | 2 | 233 | 2 | 0 | 303 | 682 | ZBTB18,LOC339529 |
| SE_02_070000020 | chr11:65476584-65500280 |
23696 | 20 | 4 | 706 | 77 | 4 | 11 | 323 | MALAT1,SCYL1,MIR612 |
| SE_02_070000019 | chr13:91136103-91168145 |
32042 | 19 | 10 | 921 | 1 | 5 | 104 | 0 | LINC00379,LINC00380 |
| SE_02_070000030 | chr14:100763609-100785963 |
22354 | 30 | 9 | 779 | 24 | 2 | 128 | 0 | DLK1,MIR2392,MEG3 |
| SE_02_070000016 | chr15:78670873-78686074 |
15201 | 16 | 12 | 405 | 55 | 18 | 53 | 0 | CHRNB4,CHRNA3 |
| SE_02_070000011 | chr17:43231496-43252462 |
20966 | 11 | 5 | 0 | 0 | 0 | 0 | 0 | RNU2-1,TMEM106A,LINC00854 |
| SE_02_070000008 | chr17:43266781-43300948 |
34167 | 8 | 9 | 0 | 0 | 0 | 0 | 0 | RNU2-1,LINC00854 |
| SE_02_070000010 | chr17:47981494-48015631 |
34137 | 10 | 17 | 873 | 127 | 1 | 0 | 79 | CDK5RAP3,PNPO,NFE2L1,PRR15L,SP2-AS1,COPZ2,MIR152 |
| SE_02_070000027 | chr2:15694052-15694913 |
861 | 27 | 1 | 38 | 1 | 0 | 5 | 0 | LOC101926966 |
| SE_02_070000003 | chr2:15808130-15811239 |
3109 | 3 | 1 | 93 | 3 | 0 | 51 | 0 | MYCNUT |
| SE_02_070000023 | chr2:15814986-15815768 |
782 | 23 | 1 | 22 | 0 | 0 | 15 | 0 | MYCNUT |
| SE_02_070000005 | chr2:15817815-15820826 |
3011 | 5 | 1 | 96 | 2 | 1 | 73 | 0 | MYCNUT |
| SE_02_070000009 | chr2:15824943-15827743 |
2800 | 9 | 1 | 105 | 1 | 1 | 45 | 0 | MYCNUT |
| SE_02_070000002 | chr2:15840700-15844912 |
4212 | 2 | 1 | 163 | 0 | 0 | 27 | 0 | MYCNUT |
| SE_02_070000015 | chr2:15845824-15847074 |
1250 | 15 | 1 | 55 | 0 | 1 | 0 | 0 | MYCNUT |
| SE_02_070000032 | chr2:15856171-15856796 |
625 | 32 | 1 | 12 | 0 | 0 | 0 | 0 | MYCNUT |
| SE_02_070000022 | chr2:15881543-15882228 |
685 | 22 | 1 | 16 | 0 | 0 | 0 | 0 | MYCNUT |
| SE_02_070000018 | chr2:15885905-15886756 |
851 | 18 | 1 | 28 | 0 | 0 | 1 | 0 | MYCNUT |
| SE_02_070000006 | chr2:15889713-15892808 |
3095 | 6 | 1 | 102 | 2 | 3 | 38 | 0 | MYCN,MYCNUT,MYCNOS |
| SE_02_070000028 | chr2:15965511-15966539 |
1028 | 28 | 2 | 39 | 0 | 0 | 9 | 0 | MYCN,MYCNUT,MYCNOS |
| SE_02_070000007 | chr2:15981581-15986957 |
5376 | 7 | 5 | 173 | 0 | 0 | 43 | 0 | MYCN,MYCNOS |
| SE_02_070000001 | chr2:16141933-16469980 |
328047 | 1 | 168 | 9702 | 90 | 28 | 1177 | 65 | GACAT3 |
| SE_02_070000017 | chr2:16538657-16549275 |
10618 | 17 | 8 | 312 | 27 | 5 | 9 | 0 | FAM49A |
| SE_02_070000004 | chr2:16565779-16658718 |
92939 | 4 | 54 | 2517 | 71 | 5 | 273 | 157 | FAM49A |
| SE_02_070000024 | chr20:58448508-58472317 |
23809 | 24 | 7 | 704 | 60 | 0 | 111 | 1122 | VAPB,APCDD1L,APCDD1L-AS1 |
| SE_02_070000012 | chr4:173517051-173538561 |
21510 | 12 | 23 | 606 | 27 | 3 | 225 | 1155 | HAND2-AS1,HAND2 |
| SE_02_070000025 | chr4:41743750-41752162 |
8412 | 25 | 7 | 227 | 2 | 3 | 166 | 661 | PHOX2B |
| SE_02_070000014 | chr4:41858086-41882635 |
24549 | 14 | 11 | 619 | 44 | 3 | 371 | 355 | LINC00682 |
| SE_02_070000021 | chr5:124735800-124749886 |
14086 | 21 | 11 | 309 | 1 | 2 | 294 | 346 | ZNF608 |
| SE_02_070000031 | chr6:79797105-79814839 |
17734 | 31 | 4 | 488 | 42 | 2 | 30 | 187 | C6ORF7 |
| SE_02_070000013 | chrX:115844328-115888829 |
44501 | 13 | 17 | 28 | 0 | 0 | 0 | 0 | DANT2 |
SE annotation visualization
Information description of sample and annotation
| Case ID: | Name:GSM3172698 |
| Input ID: | Name:GSM3172700 |
| 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 |