Variant report
| Variant | rs11589736 |
|---|---|
| Chromosome Location | chr1:220495572-220495573 |
| allele | G/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:2)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:2 , 50 per page) page:
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| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | RAD21 | chr1:220495116-220495582 | MCF-7 | breast: | n/a | chr1:220495229-220495243 |
| 2 | CTCF | chr1:220495143-220495598 | K562 | blood: | n/a | n/a |
| No data |
(count:1 , 50 per page) page:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr1:220469373..220470129-chr1:220494958..220495790,3 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000232883 | TF binding region |
rSNPs within LD-proxies of this variant (count:17)
| rs_ID | r2[population] |
|---|---|
| rs10863542 | 0.87[AMR][1000 genomes];0.87[EUR][1000 genomes] |
| rs10863543 | 0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs10863545 | 0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs11118518 | 1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs1511697 | 0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs1983247 | 0.98[AMR][1000 genomes];0.87[EUR][1000 genomes] |
| rs1983248 | 0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs2089861 | 0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs2089862 | 0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs2102572 | 0.83[EUR][1000 genomes] |
| rs4846623 | 1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs4846627 | 0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs756245 | 0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes] |
| rs879449 | 0.94[AMR][1000 genomes];0.87[EUR][1000 genomes] |
| rs907414 | 0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs925446 | 0.94[CHB][hapmap];0.90[JPT][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes] |
| rs925447 | 0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page:
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| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1001681 | chr1:220425057-220548325 | Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 9 gene(s) | inside rSNPs | diseases |
| 2 | nsv535298 | chr1:220425057-220548325 | Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 9 gene(s) | inside rSNPs | diseases |
| 3 | nsv523114 | chr1:220486349-220500958 | Enhancers Weak transcription | TF binding regionCpG islandChromatin interactive region | 2 gene(s) | inside rSNPs | diseases |
| 4 | nsv1006979 | chr1:220488188-220501518 | Enhancers Weak transcription | TF binding regionCpG islandChromatin interactive region | 2 gene(s) | inside rSNPs | diseases |
| 5 | esv16878 | chr1:220495388-220499568 | Enhancers Weak transcription | TF binding regionChromatin interactive region | 1 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:220493000-220499600 | Weak transcription | Fetal Heart | heart |
| 2 | chr1:220495000-220495600 | Enhancers | GM12878-XiMat | blood |
