Sample overview
| Species: | Human |
| Biosample type: | Cell line |
| Tissue type: | Brain |
| Data source: | NCBI GEO/SRA |
| Biosample name: | 3128_GBM |
| Sample ID: | Sample_02_0803 |
| SE ID | SE Region | Size | Rank | Element | Common SNP | eQTL | Risk SNP | TFBS | CRISPR Cas9 | Gene |
|---|---|---|---|---|---|---|---|---|---|---|
| SE_02_080300001 | chr17:77321891-77323915 |
2024 | 1 | 3 | 72 | 1 | 0 | 9 | 0 | SEPT9 |
| SE_02_080300003 | chr3:115791380-115791820 |
440 | 3 | 1 | 16 | 0 | 0 | 0 | 0 | GAP43 |
| SE_02_080300002 | chr3:159763600-159765179 |
1579 | 2 | 2 | 46 | 1 | 0 | 63 | 329 | IQCJ-SCHIP1,SCHIP1,IQCJ-SCHIP1-AS1 |
SE annotation visualization
Information description of sample and annotation
| Case ID: | Name:GSM3382185 |
| Input ID: | Name:GSM3382186 |
| 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 |