Variant report
| Variant | rs16890972 |
|---|---|
| Chromosome Location | chr6:25727448-25727449 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:21)
- CpG islands (count:0)
- Chromatin interactive region (count:6)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:21 , 50 per page) page:
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| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | POLR2A | chr6:25726265-25727575 | K562 | blood: | n/a | n/a |
| 2 | POLR2A | chr6:25726078-25727679 | K562 | blood: | n/a | n/a |
| 3 | POLR2A | chr6:25726297-25727684 | K562 | blood: | n/a | n/a |
| 4 | POLR2A | chr6:25725621-25728449 | K562 | blood: | n/a | n/a |
| 5 | PML | chr6:25726241-25727456 | K562 | blood: | n/a | n/a |
| 6 | POLR2A | chr6:25726283-25728295 | K562 | blood: | n/a | n/a |
| 7 | POLR2A | chr6:25726081-25727575 | K562 | blood: | n/a | n/a |
| 8 | POLR2A | chr6:25726276-25727598 | K562 | blood: | n/a | n/a |
| 9 | CEBPD | chr6:25725966-25727592 | K562 | blood: | n/a | n/a |
| 10 | PML | chr6:25726167-25727552 | K562 | blood: | n/a | n/a |
| 11 | TAF1 | chr6:25727317-25727579 | K562 | blood: | n/a | n/a |
| 12 | HEY1 | chr6:25725670-25728569 | K562 | blood: | n/a | n/a |
| 13 | POLR2A | chr6:25725688-25728100 | K562 | blood: | n/a | n/a |
| 14 | BCLAF1 | chr6:25725654-25727678 | K562 | blood: | n/a | chr6:25725790-25725799 |
| 15 | NR2F2 | chr6:25727201-25727663 | K562 | blood: | n/a | n/a |
| 16 | TEAD4 | chr6:25726357-25727486 | K562 | blood: | n/a | n/a |
| 17 | HEY1 | chr6:25726177-25727588 | K562 | blood: | n/a | n/a |
| 18 | POLR2A | chr6:25725813-25727544 | K562 | blood: | n/a | n/a |
| 19 | POLR2A | chr6:25725975-25727623 | K562 | blood: | n/a | n/a |
| 20 | POLR2A | chr6:25726369-25727477 | K562 | blood: | n/a | n/a |
| 21 | ZNF384 | chr6:25727306-25727491 | K562 | blood: | n/a | n/a |
| No data |
(count:6 , 50 per page) page:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr6:25724700..25728805-chr6:26024464..26033486,16 | K562 | blood: | |
| 2 | chr6:25725904..25728723-chr6:26024464..26030208,7 | K562 | blood: | |
| 3 | chr6:25726594..25729863-chr6:25991893..25994558,4 | K562 | blood: | |
| 4 | chr6:25726417..25728737-chr6:26124112..26125886,2 | K562 | blood: | |
| 5 | chr6:25725442..25728537-chr6:25991436..25993393,3 | K562 | blood: | |
| 6 | chr5:177631720..177633728-chr6:25726576..25729132,2 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| HIST1H2AA | TF binding region |
| ENSG00000180573 | Chromatin interaction |
| ENSG00000180596 | Chromatin interaction |
| ENSG00000272462 | Chromatin interaction |
| ENSG00000197451 | Chromatin interaction |
| ENSG00000124693 | Chromatin interaction |
| ENSG00000124529 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:10)
| rs_ID | r2[population] |
|---|---|
| rs10498729 | 1.00[ASW][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs16890971 | 0.91[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs16890975 | 1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs16890987 | 1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs16890989 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs28655240 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs57220361 | 0.91[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs58762565 | 0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs58845941 | 0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs6900721 | 0.83[AMR][1000 genomes];1.00[EUR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:4 , 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 | nsv883488 | chr6:25592489-25731691 | Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 16 gene(s) | inside rSNPs | diseases |
| 2 | nsv1029920 | chr6:25638507-26585842 | Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 1215 gene(s) | inside rSNPs | diseases |
| 3 | nsv538162 | chr6:25638507-26585842 | Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 1215 gene(s) | inside rSNPs | diseases |
| 4 | nsv427747 | chr6:25641380-25908218 | Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 21 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr6:25726800-25732600 | Weak transcription | iPS DF 19.11 Cell Line | embryonic stem cell |
| 2 | chr6:25727000-25727600 | Flanking Bivalent TSS/Enh | K562 | blood |
| 3 | chr6:25727400-25728000 | Enhancers | HepG2 | liver |
