Variant report
| Variant | rs6939756 |
|---|---|
| Chromosome Location | chr6:54599801-54599802 |
| 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 | chr6:54597254..54599876-chr6:54711300..54712858,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000168143 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:19)
| rs_ID | r2[population] |
|---|---|
| rs10948847 | 0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs1572593 | 0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs16885948 | 0.80[AMR][1000 genomes];0.81[EUR][1000 genomes] |
| rs2397167 | 0.83[AMR][1000 genomes];0.82[EUR][1000 genomes] |
| rs4994100 | 0.80[EUR][1000 genomes] |
| rs58302712 | 0.80[AMR][1000 genomes] |
| rs6459019 | 0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs6915244 | 0.80[AMR][1000 genomes];0.81[EUR][1000 genomes] |
| rs6929307 | 0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs6941518 | 0.83[AMR][1000 genomes];0.81[EUR][1000 genomes] |
| rs73446030 | 0.80[AMR][1000 genomes];0.81[EUR][1000 genomes] |
| rs73446036 | 0.80[AMR][1000 genomes];0.81[EUR][1000 genomes] |
| rs73446043 | 0.80[AMR][1000 genomes];0.81[EUR][1000 genomes] |
| rs7755817 | 0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs9296766 | 0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs9464126 | 0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs9464129 | 0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs9474957 | 0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs9474980 | 1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[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 | nsv885900 | chr6:54517968-54852462 | Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 13 gene(s) | inside rSNPs | diseases |
| 2 | nsv885901 | chr6:54588069-54635417 | Enhancers Weak transcription Strong transcription Flanking Active TSS | TF binding regionChromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
| 3 | nsv885902 | chr6:54588069-54656673 | Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription | TF binding regionChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr6:54599800-54600200 | Strong transcription | Breast variant Human Mammary Epithelial Cells (vHMEC) | Breast |
