Variant report
| Variant | rs213542 |
|---|---|
| Chromosome Location | chr2:234780736-234780737 |
| allele | C/T |
| 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 | SPI1 | chr2:234780666-234781351 | GM12878 | blood: | n/a | n/a |
| 2 | SPI1 | chr2:234780664-234781193 | HL-60 | blood: | n/a | n/a |
| 3 | SPI1 | chr2:234780714-234781047 | GM12891 | blood: | n/a | n/a |
| 4 | SPI1 | chr2:234780706-234781055 | GM12878 | blood: | n/a | n/a |
| 5 | SPI1 | chr2:234780711-234781049 | GM12891 | blood: | n/a | n/a |
| No data |
(count:2 , 50 per page) page:
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| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| MSL3P1 | TF binding region |
| ENSG00000224287 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:23)
| rs_ID | r2[population] |
|---|---|
| rs10929314 | 0.80[AMR][1000 genomes] |
| rs13003628 | 0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs13016127 | 0.80[AMR][1000 genomes] |
| rs169922 | 0.81[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs183331 | 0.96[CEU][hapmap];0.96[EUR][1000 genomes] |
| rs213545 | 0.93[CEU][hapmap];0.92[EUR][1000 genomes] |
| rs2215172 | 0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs2302156 | 0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes] |
| rs4663339 | 0.96[CEU][hapmap];0.96[EUR][1000 genomes] |
| rs501145 | 0.96[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes] |
| rs525359 | 0.96[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes] |
| rs556691 | 0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes] |
| rs580045 | 0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes] |
| rs619929 | 0.96[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes] |
| rs626110 | 0.96[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes] |
| rs637082 | 0.95[ASN][1000 genomes] |
| rs638071 | 0.93[ASN][1000 genomes] |
| rs6431643 | 0.96[CEU][hapmap];0.96[EUR][1000 genomes] |
| rs6431644 | 0.89[CEU][hapmap];0.96[EUR][1000 genomes] |
| rs650570 | 0.94[ASN][1000 genomes] |
| rs650700 | 0.95[ASN][1000 genomes] |
| rs654279 | 0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes] |
| rs7596657 | 0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1013712 | chr2:234558457-235495825 | Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 41 gene(s) | inside rSNPs | diseases |
| 2 | nsv532476 | chr2:234595695-235134381 | Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 37 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr2:234780200-234781000 | Weak transcription | Primary hematopoietic stem cells G-CSF-mobilized Female | -- |
| 2 | chr2:234780200-234781200 | Enhancers | Primary hematopoietic stem cells G-CSF-mobilized Male | -- |
