Variant report
| Variant | rs13397175 |
|---|---|
| Chromosome Location | chr2:55661230-55661231 |
| allele | A/C |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:4)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:4 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr2:55458753..55460899-chr2:55659427..55661705,2 | MCF-7 | breast: | |
| 2 | chr2:55463171..55466180-chr2:55659869..55661423,3 | MCF-7 | breast: | |
| 3 | chr2:55652771..55655244-chr2:55659480..55661281,2 | K562 | blood: | |
| 4 | chr2:55653744..55655531-chr2:55659781..55661813,3 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000162994 | Chromatin interaction |
| ENSG00000143947 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:16)
| rs_ID | r2[population] |
|---|---|
| rs10169760 | 1.00[AMR][1000 genomes] |
| rs10175125 | 0.95[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs10185921 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs10469925 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs10469926 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs10469927 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs13393046 | 0.87[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs13394244 | 0.95[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs13405484 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs13407643 | 1.00[AMR][1000 genomes] |
| rs13407739 | 0.95[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs13410452 | 0.95[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs13414738 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs13415672 | 1.00[YRI][hapmap];1.00[AMR][1000 genomes] |
| rs13424427 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs9309265 | 1.00[AMR][1000 genomes] |
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 | nsv1006170 | chr2:55530179-55809251 | Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 29 gene(s) | inside rSNPs | diseases |
| 2 | nsv520581 | chr2:55622825-55903016 | Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 42 gene(s) | inside rSNPs | diseases |
| 3 | nsv531374 | chr2:55653723-56299784 | Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 56 gene(s) | inside rSNPs | diseases |
| 4 | nsv961778 | chr2:55659501-55668562 | Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS | TF binding regionChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr2:55660600-55661400 | Enhancers | HepG2 | liver |
