Variant report
| Variant | rs13268738 |
|---|---|
| Chromosome Location | chr8:87673711-87673712 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:1 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr8:87668814..87670322-chr8:87672192..87674304,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000221137 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:18)
| rs_ID | r2[population] |
|---|---|
| rs10094222 | 0.82[CHB][hapmap];0.95[JPT][hapmap] |
| rs1009574 | 0.91[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes] |
| rs10216710 | 0.86[CHB][hapmap];0.95[JPT][hapmap] |
| rs10216953 | 0.85[CHB][hapmap];0.95[JPT][hapmap] |
| rs13258590 | 0.86[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap] |
| rs13278423 | 0.81[JPT][hapmap] |
| rs1441243 | 0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap] |
| rs16916427 | 0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap] |
| rs16916907 | 0.81[JPT][hapmap] |
| rs2013536 | 0.86[CHD][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes] |
| rs2885471 | 0.81[AMR][1000 genomes] |
| rs3735967 | 0.81[CHD][hapmap];0.91[JPT][hapmap] |
| rs3779790 | 0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes] |
| rs4960985 | 0.83[CHD][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes] |
| rs59109039 | 0.86[AFR][1000 genomes];0.93[ASN][1000 genomes] |
| rs7842410 | 0.82[CHB][hapmap];0.83[CHD][hapmap] |
| rs9297941 | 0.85[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap] |
| rs978134 | 0.81[JPT][hapmap] |
Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1023510 | chr8:87429001-87874948 | Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 31 gene(s) | inside rSNPs | diseases |
| 2 | nsv981963 | chr8:87671867-87673955 | Enhancers | TF binding regionChromatin interactive region | 2 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs13268738 | RIPK2 | cis | parietal | SCAN |
| rs13268738 | CNGB3 | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr8:87673200-87673800 | Enhancers | H9 Derived Neuron Cultured Cells | ES cell derived |
