Variant report
| Variant | rs17223034 |
|---|---|
| Chromosome Location | chr20:52923695-52923696 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:9)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:9 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr20:52902315..52904046-chr20:52922393..52924271,2 | MCF-7 | breast: | |
| 2 | chr20:52922776..52924284-chr20:52931074..52933006,2 | MCF-7 | breast: | |
| 3 | chr20:52824550..52826498-chr20:52922860..52925164,2 | MCF-7 | breast: | |
| 4 | chr20:52923632..52926364-chr20:52926650..52929482,4 | MCF-7 | breast: | |
| 5 | chr20:52911450..52915662-chr20:52921093..52925920,4 | MCF-7 | breast: | |
| 6 | chr20:52823568..52826063-chr20:52923324..52925181,2 | MCF-7 | breast: | |
| 7 | chr20:52897965..52899622-chr20:52923358..52924887,2 | MCF-7 | breast: | |
| 8 | chr20:52922402..52924055-chr20:52929439..52931142,2 | MCF-7 | breast: | |
| 9 | chr20:52892335..52894745-chr20:52921772..52923928,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000101132 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:8)
| rs_ID | r2[population] |
|---|---|
| rs1477736 | 0.84[EUR][1000 genomes] |
| rs17222492 | 1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes] |
| rs17313921 | 1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs2023531 | 0.89[MEX][hapmap] |
| rs2797968 | 0.83[AMR][1000 genomes];0.95[EUR][1000 genomes] |
| rs28515941 | 0.87[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs28610574 | 1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs6023080 | 0.89[MEX][hapmap] |
Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv586224 | chr20:52474850-53279490 | Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 338 gene(s) | inside rSNPs | diseases |
| 2 | nsv834010 | chr20:52759824-52932939 | Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 119 gene(s) | inside rSNPs | diseases |
| 3 | nsv834011 | chr20:52858341-53086042 | Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS | Chromatin interactive regionlncRNA | 55 gene(s) | inside rSNPs | diseases |
| 4 | nsv834012 | chr20:52921007-53097177 | Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 43 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:5)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs17223034 | GCNT7 | cis | parietal | SCAN |
| rs17223034 | DOK5 | cis | parietal | SCAN |
| rs17223034 | PFDN4 | cis | parietal | SCAN |
| rs17223034 | LOC284751 | cis | parietal | SCAN |
| rs17223034 | RAE1 | cis | cerebellum | SCAN |
Chromatin state (count:0 , 50 per page) page:
| No data |
