Variant report
| Variant | rs7814843 |
|---|---|
| Chromosome Location | chr8:125929876-125929877 |
| allele | C/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:17)
- CpG islands (count:0)
- Chromatin interactive region (count:6)
- 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 | HDAC2 | chr8:125929670-125929939 | HepG2 | liver: | n/a | chr8:125929879-125929888 |
| 2 | HNF4A | chr8:125929707-125930029 | HepG2 | liver: | n/a | chr8:125929841-125929856 |
| 3 | FOXA1 | chr8:125929710-125930056 | HepG2 | liver: | n/a | n/a |
| 4 | EP300 | chr8:125929672-125930056 | HepG2 | liver: | n/a | chr8:125929879-125929889 |
| 5 | FOXA2 | chr8:125929468-125930222 | HepG2 | liver: | n/a | n/a |
| 6 | RXRA | chr8:125929723-125930023 | HepG2 | liver: | n/a | chr8:125929842-125929855 chr8:125929842-125929855 chr8:125929842-125929855 chr8:125930015-125930022 chr8:125929839-125929859 chr8:125929841-125929857 |
| 7 | TEAD4 | chr8:125929703-125930132 | HepG2 | liver: | n/a | n/a |
| 8 | BHLHE40 | chr8:125929844-125930075 | HepG2 | liver: | n/a | n/a |
| 9 | EP300 | chr8:125929711-125930041 | HepG2 | liver: | n/a | chr8:125929879-125929889 |
| 10 | FOXA2 | chr8:125929688-125930042 | HepG2 | liver: | n/a | n/a |
| 11 | HNF4G | chr8:125929716-125930009 | HepG2 | liver: | n/a | chr8:125929840-125929855 |
| 12 | NFIC | chr8:125929726-125930075 | HepG2 | liver: | n/a | n/a |
| 13 | FOXA1 | chr8:125929570-125930180 | HepG2 | liver: | n/a | n/a |
| 14 | FOXA1 | chr8:125929568-125930130 | HepG2 | liver: | n/a | n/a |
| 15 | SP1 | chr8:125929663-125930099 | HepG2 | liver: | n/a | n/a |
| 16 | HNF4A | chr8:125929644-125929957 | HepG2 | liver: | n/a | chr8:125929841-125929856 |
| 17 | FOXA1 | chr8:125929612-125930007 | HepG2 | liver: | n/a | n/a |
| No data |
(count:6 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr8:125928560..125931491-chr8:125949569..125951872,2 | MCF-7 | breast: | |
| 2 | chr8:125869478..125872586-chr8:125926416..125930050,3 | MCF-7 | breast: | |
| 3 | chr8:125903181..125907429-chr8:125925929..125929993,4 | K562 | blood: | |
| 4 | chr8:125928235..125930330-chr8:125931694..125933573,2 | K562 | blood: | |
| 5 | chr8:125928423..125931250-chr8:125983352..125985484,3 | MCF-7 | breast: | |
| 6 | chr8:125928235..125930086-chr8:125931694..125934034,2 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000250428 | TF binding region |
| ENSG00000250428 | Chromatin interaction |
| ENSG00000255080 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:18)
| rs_ID | r2[population] |
|---|---|
| rs1052291 | 1.00[ASN][1000 genomes] |
| rs11775219 | 1.00[ASN][1000 genomes] |
| rs11777190 | 1.00[ASN][1000 genomes] |
| rs11778786 | 1.00[ASN][1000 genomes] |
| rs11778814 | 1.00[ASN][1000 genomes] |
| rs11780865 | 1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];1.00[ASN][1000 genomes] |
| rs11787203 | 1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes] |
| rs11993071 | 0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes] |
| rs17304872 | 1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];1.00[ASN][1000 genomes] |
| rs17305012 | 1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes] |
| rs17396442 | 1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.97[ASN][1000 genomes] |
| rs2077670 | 1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.97[ASN][1000 genomes] |
| rs34739489 | 0.97[ASN][1000 genomes] |
| rs56073554 | 1.00[ASN][1000 genomes] |
| rs6989608 | 1.00[ASN][1000 genomes] |
| rs6990611 | 1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap] |
| rs6997550 | 0.97[ASN][1000 genomes] |
| rs7009560 | 1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes] |
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 | nsv891434 | chr8:125630655-126324432 | Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 80 gene(s) | inside rSNPs | diseases |
| 2 | nsv1030803 | chr8:125868684-125969635 | Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 36 gene(s) | inside rSNPs | diseases |
| 3 | nsv1024405 | chr8:125868684-125971035 | Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 36 gene(s) | inside rSNPs | diseases |
| 4 | nsv1020502 | chr8:125868684-125972572 | Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 36 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs7814843 | SQLE | cis | cerebellum | SCAN |
| rs7814843 | NSMCE2 | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr8:125925600-125931200 | Weak transcription | Monocytes-CD14+_RO01746 | blood |
| 2 | chr8:125929600-125931400 | Enhancers | HepG2 | liver |
| 3 | chr8:125929800-125930400 | Enhancers | Thymus | Thymus |
| 4 | chr8:125929800-125933000 | Weak transcription | K562 | blood |
