Variant report
| Variant | rs12525588 |
|---|---|
| Chromosome Location | chr6:161097590-161097591 |
| allele | A/C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:17)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:17 , 50 per page) page:
1
| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | BCL11A | chr6:161097429-161097636 | GM12878 | blood: | n/a | n/a |
| 2 | PAX5 | chr6:161097252-161097853 | GM12878 | blood: | n/a | n/a |
| 3 | IRF4 | chr6:161097383-161097696 | GM12878 | blood: | n/a | n/a |
| 4 | IRF4 | chr6:161097347-161097663 | GM12878 | blood: | n/a | n/a |
| 5 | EP300 | chr6:161097250-161097792 | GM12878 | blood: | n/a | n/a |
| 6 | SP1 | chr6:161097415-161097696 | GM12878 | blood: | n/a | n/a |
| 7 | TCF3 | chr6:161097312-161097715 | GM12878 | blood: | n/a | n/a |
| 8 | NFIC | chr6:161097328-161097656 | GM12878 | blood: | n/a | n/a |
| 9 | EBF1 | chr6:161097418-161097686 | GM12878 | blood: | n/a | n/a |
| 10 | POU2F2 | chr6:161097463-161097598 | GM12878 | blood: | n/a | n/a |
| 11 | TCF3 | chr6:161097466-161097626 | GM12878 | blood: | n/a | n/a |
| 12 | TCF12 | chr6:161097426-161097626 | GM12878 | blood: | n/a | n/a |
| 13 | BATF | chr6:161097398-161097686 | GM12878 | blood: | n/a | n/a |
| 14 | TCF12 | chr6:161097439-161097693 | GM12878 | blood: | n/a | n/a |
| 15 | PAX5 | chr6:161097429-161097698 | GM12878 | blood: | n/a | n/a |
| 16 | PAX5 | chr6:161097434-161097695 | GM12878 | blood: | n/a | n/a |
| 17 | EBF1 | chr6:161097381-161097765 | GM12878 | blood: | n/a | n/a |
| No data |
| No data |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000243831 | TF binding region |
rSNPs within LD-proxies of this variant (count:29)
| rs_ID | r2[population] |
|---|---|
| rs12523781 | 0.87[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs12526465 | 1.00[ASN][1000 genomes] |
| rs12529361 | 1.00[ASN][1000 genomes] |
| rs1358753 | 0.86[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs1358754 | 0.93[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes] |
| rs17557261 | 1.00[ASN][1000 genomes] |
| rs1998043 | 0.85[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs1998044 | 0.92[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs1998045 | 0.86[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs2115868 | 1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs41269844 | 1.00[ASN][1000 genomes] |
| rs41269878 | 1.00[ASN][1000 genomes] |
| rs4252051 | 1.00[ASN][1000 genomes] |
| rs4252052 | 1.00[ASN][1000 genomes] |
| rs4252053 | 1.00[ASN][1000 genomes] |
| rs4348293 | 0.92[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs5014650 | 1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs56090213 | 0.87[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs7758766 | 1.00[ASN][1000 genomes] |
| rs7759633 | 1.00[ASN][1000 genomes] |
| rs9456575 | 1.00[ASN][1000 genomes] |
| rs9457991 | 0.83[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs9457993 | 1.00[ASN][1000 genomes] |
| rs9457997 | 0.82[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs9457998 | 1.00[ASN][1000 genomes] |
| rs9458002 | 1.00[ASN][1000 genomes] |
| rs9458003 | 1.00[ASN][1000 genomes] |
| rs9458004 | 1.00[ASN][1000 genomes] |
| rs9458009 | 0.94[CEU][hapmap];1.00[JPT][hapmap] |
Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | esv2758089 | chr6:160372244-161234665 | Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 30 gene(s) | inside rSNPs | diseases |
| 2 | esv2759484 | chr6:160372244-161234665 | Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 30 gene(s) | inside rSNPs | diseases |
| 3 | nsv605005 | chr6:161069941-161152449 | Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 6 gene(s) | inside rSNPs | diseases |
| 4 | nsv969465 | chr6:161097287-161098379 | Weak transcription Enhancers | TF binding regionCpG island | 1 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr6:161087600-161100200 | Weak transcription | Right Atrium | heart |
| 2 | chr6:161091000-161098200 | Weak transcription | Liver | Liver |
