Variant report
| Variant | rs60312537 |
|---|---|
| Chromosome Location | chr2:55680440-55680441 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:5)
- CpG islands (count:0)
- Chromatin interactive region (count:2)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:5 , 50 per page) page:
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| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | PAX5 | chr2:55680086-55680503 | GM12878 | blood: | n/a | chr2:55680274-55680283 chr2:55680274-55680292 chr2:55680273-55680290 chr2:55680273-55680292 |
| 2 | PAX5 | chr2:55680107-55680553 | GM12892 | blood: | n/a | chr2:55680274-55680283 chr2:55680274-55680292 chr2:55680273-55680290 chr2:55680273-55680292 |
| 3 | PAX5 | chr2:55680080-55680465 | GM12878 | blood: | n/a | chr2:55680274-55680283 chr2:55680274-55680292 chr2:55680273-55680290 chr2:55680273-55680292 |
| 4 | PAX5 | chr2:55680009-55680561 | GM12878 | blood: | n/a | chr2:55680274-55680283 chr2:55680274-55680292 chr2:55680273-55680290 chr2:55680273-55680292 |
| 5 | PAX5 | chr2:55680019-55680509 | GM12891 | blood: | n/a | chr2:55680274-55680283 chr2:55680274-55680292 chr2:55680273-55680290 chr2:55680273-55680292 |
| No data |
(count:2 , 50 per page) page:
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| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| RNU6-775P | TF binding region |
| ENSG00000238619 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:21)
| rs_ID | r2[population] |
|---|---|
| rs10496047 | 0.80[EUR][1000 genomes] |
| rs12471135 | 0.87[EUR][1000 genomes] |
| rs12472098 | 0.87[EUR][1000 genomes] |
| rs1454426 | 0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs17792798 | 0.88[EUR][1000 genomes] |
| rs17792822 | 0.88[EUR][1000 genomes] |
| rs41281507 | 0.88[EUR][1000 genomes] |
| rs4671247 | 0.88[EUR][1000 genomes] |
| rs4672053 | 0.88[EUR][1000 genomes] |
| rs4672057 | 0.81[EUR][1000 genomes] |
| rs55850643 | 0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs55987004 | 0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs56227318 | 0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs56286204 | 0.81[EUR][1000 genomes] |
| rs56299972 | 0.80[EUR][1000 genomes] |
| rs56409619 | 0.85[AFR][1000 genomes];1.00[ASN][1000 genomes] |
| rs56769899 | 0.83[EUR][1000 genomes] |
| rs6741902 | 0.80[EUR][1000 genomes] |
| rs6752098 | 0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs72801524 | 0.85[AFR][1000 genomes];1.00[ASN][1000 genomes] |
| rs7600034 | 0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:5 , 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 | esv1802545 | chr2:55668771-55687618 | Enhancers Active TSS Flanking Active TSS Weak transcription | TF binding regionCpG islandChromatin interactive region | 2 gene(s) | inside rSNPs | diseases |
| 5 | esv3365493 | chr2:55677866-55682407 | Weak transcription Enhancers | TF binding regionChromatin interactive region | 1 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr2:55679200-55681400 | Weak transcription | Foreskin Keratinocyte Primary Cells skin03 | Skin |
| 2 | chr2:55680000-55680600 | Enhancers | GM12878-XiMat | blood |
