Variant report
| Variant | rs1343488 |
|---|---|
| Chromosome Location | chr6:78202442-78202443 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:13)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:13 , 50 per page) page:
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| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | FOXA1 | chr6:78202230-78202691 | HepG2 | liver: | n/a | n/a |
| 2 | FOXA1 | chr6:78202212-78202656 | HepG2 | liver: | n/a | n/a |
| 3 | FOXA1 | chr6:78202307-78202561 | HepG2 | liver: | n/a | n/a |
| 4 | MYBL2 | chr6:78202250-78202543 | HepG2 | liver: | n/a | n/a |
| 5 | FOXA2 | chr6:78202341-78202694 | A549 | lung: | n/a | n/a |
| 6 | EP300 | chr6:78202227-78202595 | HepG2 | liver: | n/a | n/a |
| 7 | FOXA2 | chr6:78202361-78202651 | A549 | lung: | n/a | n/a |
| 8 | SP1 | chr6:78202257-78202615 | A549 | lung: | n/a | n/a |
| 9 | FOXA1 | chr6:78202303-78202618 | HepG2 | liver: | n/a | n/a |
| 10 | FOXA2 | chr6:78202304-78202597 | HepG2 | liver: | n/a | n/a |
| 11 | TCF12 | chr6:78202244-78202607 | A549 | lung: | n/a | n/a |
| 12 | GATA3 | chr6:78202263-78202743 | MCF-7 | breast: | n/a | chr6:78202533-78202554 chr6:78202381-78202393 |
| 13 | NFIC | chr6:78202207-78202625 | HepG2 | liver: | n/a | n/a |
| No data |
| No data |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| RPS6P7 | TF binding region |
rSNPs within LD-proxies of this variant (count:10)
| rs_ID | r2[population] |
|---|---|
| rs1145835 | 1.00[AFR][1000 genomes] |
| rs12173930 | 1.00[AFR][1000 genomes] |
| rs12524589 | 1.00[AFR][1000 genomes];0.91[EUR][1000 genomes] |
| rs13204128 | 1.00[AFR][1000 genomes] |
| rs1778258 | 1.00[CEU][hapmap] |
| rs62418262 | 1.00[AFR][1000 genomes];0.91[EUR][1000 genomes] |
| rs6297 | 1.00[AFR][1000 genomes] |
| rs7748725 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs9352485 | 1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs9359274 | 1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:9 , 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 | nsv1017082 | chr6:77585310-78258237 | Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 5 gene(s) | inside rSNPs | diseases |
| 2 | nsv534282 | chr6:77764575-78351994 | Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
| 3 | nsv1034979 | chr6:77781244-78426249 | Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 5 gene(s) | inside rSNPs | diseases |
| 4 | nsv538324 | chr6:77781244-78426249 | Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 5 gene(s) | inside rSNPs | diseases |
| 5 | nsv1015307 | chr6:77902559-78352291 | Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | diseases |
| 6 | nsv1028259 | chr6:78059491-78709871 | Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
| 7 | nsv538325 | chr6:78059491-78709871 | Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
| 8 | esv2758062 | chr6:78100020-78283042 | Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | diseases |
| 9 | esv2759445 | chr6:78100020-78283042 | Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats 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 | chr6:78200600-78203600 | Enhancers | Stomach Mucosa | stomach |
| 2 | chr6:78201200-78202600 | Strong transcription | HUVEC | blood vessel |
| 3 | chr6:78202000-78203000 | Enhancers | HepG2 | liver |
