Variant report
| Variant | rs61923303 |
|---|---|
| Chromosome Location | chr12:60809657-60809658 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:4)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:4 , 50 per page) page:
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| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | CEBPB | chr12:60809161-60809716 | IMR90 | lung: | n/a | n/a |
| 2 | KAP1 | chr12:60809460-60809836 | HEK293 | kidney: | n/a | n/a |
| 3 | GATA2 | chr12:60809171-60809775 | HUVEC | blood vessel: | n/a | n/a |
| 4 | CBX3 | chr12:60809451-60809945 | HCT-116 | colon: | 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 | chr12:60809569..60811831-chr12:60814159..60815747,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000257865 | TF binding region |
rSNPs within LD-proxies of this variant (count:13)
| rs_ID | r2[population] |
|---|---|
| rs10877427 | 0.83[ASN][1000 genomes] |
| rs10877428 | 0.83[ASN][1000 genomes] |
| rs11173452 | 0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes] |
| rs11173462 | 0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes] |
| rs11173463 | 0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes] |
| rs11173469 | 0.89[EUR][1000 genomes] |
| rs11173470 | 0.86[EUR][1000 genomes] |
| rs11173471 | 0.89[EUR][1000 genomes] |
| rs12228176 | 0.84[EUR][1000 genomes] |
| rs1857729 | 0.83[ASN][1000 genomes] |
| rs2655898 | 0.83[ASN][1000 genomes] |
| rs59654269 | 0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs61923302 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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 | nsv1054287 | chr12:60601870-60861866 | Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 5 gene(s) | inside rSNPs | diseases |
| 2 | nsv1047466 | chr12:60702221-61521156 | Active TSS Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 8 gene(s) | inside rSNPs | diseases |
| 3 | nsv832432 | chr12:60801619-60968907 | Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr12:60808800-60810400 | Strong transcription | Breast variant Human Mammary Epithelial Cells (vHMEC) | Breast |
