Sample overview
| Species: | Human |
| Biosample type: | Primary cell |
| Tissue type: | Peripheral blood |
| Data source: | NCBI GEO/SRA |
| Biosample name: | peripheral blood monocyte-derived SC cells |
| Sample ID: | Sample_02_1441 |
| SE ID | SE Region | Size | Rank | Element | Common SNP | eQTL | Risk SNP | TFBS | CRISPR Cas9 | Gene |
|---|---|---|---|---|---|---|---|---|---|---|
| SE_02_144100019 | chr1:149995150-150000532 |
5382 | 19 | 2 | 123 | 10 | 0 | 20 | 0 | OTUD7B |
| SE_02_144100020 | chr10:117057361-117061686 |
4325 | 20 | 2 | 102 | 10 | 1 | 0 | 0 | SHTN1 |
| SE_02_144100013 | chr11:120339800-120348935 |
9135 | 13 | 3 | 215 | 13 | 2 | 39 | 0 | ARHGEF12,TMEM136 |
| SE_02_144100011 | chr11:3653871-3654760 |
889 | 11 | 1 | 8 | 0 | 0 | 0 | 0 | ART1,ART5,CHRNA10,TRPC2 |
| SE_02_144100009 | chr12:106908473-106917732 |
9259 | 9 | 4 | 253 | 45 | 1 | 19 | 0 | TMEM263 |
| SE_02_144100004 | chr13:99040963-99056882 |
15919 | 4 | 5 | 428 | 50 | 5 | 33 | 0 | DOCK9,DOCK9-AS2,RNU6-83P |
| SE_02_144100002 | chr13:99133828-99162167 |
28339 | 2 | 9 | 761 | 70 | 1 | 13 | 0 | DOCK9-AS2,UBAC2-AS1,DOCK9,UBAC2 |
| SE_02_144100008 | chr15:94577660-94591304 |
13644 | 8 | 5 | 443 | 0 | 0 | 51 | 0 | MCTP2,LINC01580 |
| SE_02_144100018 | chr15:95443631-95449654 |
6023 | 18 | 2 | 171 | 2 | 0 | 10 | 0 | LINC00924 |
| SE_02_144100021 | chr15:97072892-97082035 |
9143 | 21 | 2 | 245 | 1 | 0 | 92 | 0 | SPATA8 |
| SE_02_144100005 | chr17:26882099-26884642 |
2543 | 5 | 1 | 0 | 0 | 0 | 0 | 0 | MIR4522,KSR1 |
| SE_02_144100017 | chr2:149896857-149902469 |
5612 | 17 | 2 | 147 | 0 | 0 | 1 | 0 | MMADHC |
| SE_02_144100022 | chr2:89849088-89852899 |
3811 | 22 | 2 | 133 | 17 | 0 | 0 | 153 | |
| SE_02_144100025 | chr2:94501855-94502524 |
669 | 25 | 1 | 0 | 0 | 0 | 0 | 0 | LOC100133920 |
| SE_02_144100026 | chr20:22139606-22140622 |
1016 | 26 | 1 | 23 | 0 | 1 | 0 | 0 | LINC01432 |
| SE_02_144100023 | chr20:28497581-28498173 |
592 | 23 | 1 | 0 | 1 | 0 | 0 | 0 | FRG1CP |
| SE_02_144100015 | chr20:47894711-47896040 |
1329 | 15 | 1 | 18 | 0 | 0 | 0 | 0 | LINC01523 |
| SE_02_144100006 | chr21:9006280-9021332 |
15052 | 6 | 3 | 259 | 2 | 0 | 0 | 0 | TEKT4P2 |
| SE_02_144100027 | chr5:142356279-142358532 |
2253 | 27 | 2 | 73 | 5 | 0 | 23 | 0 | LOC101926941,SPRY4,SPRY4-IT1 |
| SE_02_144100012 | chr5:145950027-145955896 |
5869 | 12 | 5 | 149 | 8 | 0 | 13 | 0 | SH3RF2 |
| SE_02_144100007 | chr5:38448861-38459008 |
10147 | 7 | 3 | 293 | 8 | 3 | 29 | 133 | EGFLAM,EGFLAM-AS2 |
| SE_02_144100003 | chr5:73144992-73168518 |
23526 | 3 | 8 | 646 | 40 | 8 | 18 | 0 | TMEM171,TMEM174 |
| SE_02_144100010 | chr7:13844676-13854225 |
9549 | 10 | 3 | 293 | 13 | 2 | 35 | 0 | ETV1 |
| SE_02_144100014 | chr7:38984544-38996195 |
11651 | 14 | 2 | 271 | 17 | 0 | 39 | 67 | POU6F2 |
| SE_02_144100001 | chr8:140985509-141049481 |
63972 | 1 | 15 | 2016 | 59 | 1 | 84 | 162 | PTK2 |
| SE_02_144100024 | chrUn_GL000218v1:120575-124111 |
3536 | 24 | 2 | 0 | 0 | 0 | 0 | 0 | LOC100233156 |
| SE_02_144100016 | chrUn_GL000219v1:151795-156117 |
4322 | 16 | 2 | 0 | 0 | 0 | 0 | 0 | LOC283788 |
SE annotation visualization
Information description of sample and annotation
| Case ID: | Name:GSM5124337 |
| Input ID: | Name:GSM5124341 |
| 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 |