Variant report
| Variant | rs56669998 |
|---|---|
| Chromosome Location | chr4:99873884-99873885 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:1)
- CpG islands (count:0)
- Chromatin interactive region (count:4)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:1 , 50 per page) page:
1
| No data |
(count:4 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr4:99866310..99868814-chr4:99873787..99876130,2 | MCF-7 | breast: | |
| 2 | chr4:99873824..99875592-chr4:99885259..99887422,2 | K562 | blood: | |
| 3 | chr4:99849556..99852352-chr4:99871791..99874229,4 | K562 | blood: | |
| 4 | chr4:99849844..99852352-chr4:99870483..99874229,4 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| FAM177A1P1 | TF binding region |
| ENSG00000263923 | Chromatin interaction |
| ENSG00000151247 | Chromatin interaction |
| ENSG00000238449 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:16)
| rs_ID | r2[population] |
|---|---|
| rs10516438 | 1.00[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs11726503 | 0.80[ASN][1000 genomes] |
| rs12507214 | 0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs12649066 | 0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs12651447 | 0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs2028685 | 0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs2028686 | 0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs2028687 | 0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs3749547 | 0.92[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs55807127 | 0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs66467917 | 0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs66761677 | 0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs66809909 | 0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs67517620 | 0.88[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs72692611 | 0.84[EUR][1000 genomes] |
| rs7654109 | 0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[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 | nsv1009017 | chr4:99669441-100406394 | Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 57 gene(s) | inside rSNPs | diseases |
| 2 | nsv879654 | chr4:99748988-99877402 | Weak transcription Enhancers Strong transcription Active TSS Flanking 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 | 31 gene(s) | inside rSNPs | diseases |
| 3 | nsv822667 | chr4:99873553-99874052 | Enhancers Weak transcription | TF binding regionChromatin interactive region | 4 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr4:99872600-99874000 | Weak transcription | Adipose Derived Mesenchymal Stem Cell Cultured Cells | ES cell derived |
