Variant report
Variant | rs1558738 |
---|---|
Chromosome Location | chr20:15536007-15536008 |
allele | A/G |
Outlinks | Ensembl   UCSC |
- TF binding region (count:3)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:3 , 50 per page) page:
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No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
---|---|---|---|---|---|---|
1 | CTCF | chr20:15535920-15536070 | GM12871 | blood: | n/a | n/a |
2 | EP300 | chr20:15535911-15537224 | SK-N-SH | brain: | n/a | chr20:15536981-15536991 |
3 | GATA2 | chr20:15535716-15536865 | SH-SY5Y | brain: | n/a | chr20:15536607-15536616 chr20:15535875-15535886 |
No data |
No data |
No data |
No data |
No data |
Variant related genes | Relation type |
---|---|
ENSG00000225181 | TF binding region |
rs_ID | r2[population] |
---|---|
rs1233715 | 0.82[CHB][hapmap];0.95[JPT][hapmap] |
rs1233720 | 0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap] |
rs1233722 | 0.96[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap] |
rs1233723 | 0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap] |
rs1233724 | 0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap] |
rs1233728 | 0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes] |
rs1233729 | 0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes] |
rs1233730 | 0.82[CHB][hapmap];0.80[CHD][hapmap];0.81[JPT][hapmap] |
rs1233731 | 0.82[CHB][hapmap];0.80[CHD][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap] |
rs1233736 | 0.84[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes] |
rs1233774 | 0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes] |
rs1233775 | 0.80[CEU][hapmap] |
rs1233777 | 0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes] |
rs1233778 | 0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes] |
rs1233779 | 0.80[CEU][hapmap] |
rs1233780 | 0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes] |
rs1547972 | 0.87[CEU][hapmap] |
rs6043347 | 0.87[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes] |
rs6043359 | 0.92[CEU][hapmap];0.80[TSI][hapmap];0.84[AMR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:5 , 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 | nsv1062252 | chr20:14964258-15547739 | Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 8 gene(s) | inside rSNPs | diseases |
2 | nsv544206 | chr20:14964258-15547739 | Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 8 gene(s) | inside rSNPs | diseases |
3 | nsv869328 | chr20:15325423-16213898 | Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 9 gene(s) | inside rSNPs | diseases |
4 | esv2751909 | chr20:15489871-15656007 | Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats | TF binding regionChromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
5 | nsv962630 | chr20:15535832-15538767 | Weak transcription Enhancers | TF binding region | 1 gene(s) | inside rSNPs | diseases |
No. | Chromosome Location | Chromatin state | Cell line | Tissue |
---|---|---|---|---|
1 | chr20:15533400-15541600 | Weak transcription | ES-UCSF4 Cell Line | embryonic stem cell |
2 | chr20:15533800-15541600 | Weak transcription | Fetal Brain Male | brain |
3 | chr20:15536000-15537000 | Enhancers | Fetal Stomach | stomach |