Variant report
| Variant | rs11782542 |
|---|---|
| Chromosome Location | chr8:90881910-90881911 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:6)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:6 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr8:90880816..90883568-chr8:90884439..90886830,2 | K562 | blood: | |
| 2 | chr8:90876426..90880425-chr8:90881590..90883827,5 | MCF-7 | breast: | |
| 3 | chr8:90877915..90882075-chr8:90892079..90895246,4 | MCF-7 | breast: | |
| 4 | chr8:90879570..90882252-chr8:90898908..90901899,2 | MCF-7 | breast: | |
| 5 | chr8:90879148..90883716-chr8:90914066..90917336,5 | MCF-7 | breast: | |
| 6 | chr8:90881870..90883463-chr8:90886720..90888927,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000164823 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:10)
| rs_ID | r2[population] |
|---|---|
| rs12334945 | 0.91[CEU][hapmap];0.90[EUR][1000 genomes] |
| rs379174 | 0.82[CHB][hapmap] |
| rs381948 | 0.82[CHB][hapmap] |
| rs393781 | 0.82[CHB][hapmap] |
| rs398957 | 0.82[CHB][hapmap] |
| rs400613 | 0.82[CHB][hapmap] |
| rs404292 | 0.82[CHB][hapmap] |
| rs428441 | 0.82[CHB][hapmap] |
| rs431623 | 0.82[CHB][hapmap] |
| rs4960980 | 0.85[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv933502 | chr8:90702392-91049100 | Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 62 gene(s) | inside rSNPs | diseases |
| 2 | nsv934114 | chr8:90720182-90999106 | Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 58 gene(s) | inside rSNPs | diseases |
| 3 | nsv891182 | chr8:90785685-90888786 | Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 12 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:3)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs11782542 | RIPK2 | cis | cerebellum | SCAN |
| rs11782542 | CALB1 | cis | cerebellum | SCAN |
| rs11782542 | RIPK2 | cis | parietal | SCAN |
Chromatin state (count:0 , 50 per page) page:
| No data |
