Variant report
| Variant | rs10439485 |
|---|---|
| Chromosome Location | chr2:58478609-58478610 |
| allele | C/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:28)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:1)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:28 , 50 per page) page:
1
| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | CTCF | chr2:58478594-58478627 | Fibrobl | skin: | n/a | n/a |
| 2 | POLR2A | chr2:58478569-58479002 | Hela-S3 | cervix: | n/a | n/a |
| 3 | GABPA | chr2:58478490-58478928 | Hela-S3 | cervix: | n/a | n/a |
| 4 | POLR2A | chr2:58478548-58478742 | MCF-7 | breast: | n/a | n/a |
| 5 | GABPA | chr2:58478573-58478901 | HepG2 | liver: | n/a | n/a |
| 6 | TAF1 | chr2:58478520-58478905 | HepG2 | liver: | n/a | n/a |
| 7 | ZBTB33 | chr2:58478526-58479270 | K562 | blood: | n/a | n/a |
| 8 | TAF1 | chr2:58478595-58478936 | H1-hESC | embryonic stem cell: | n/a | n/a |
| 9 | HEY1 | chr2:58478571-58478992 | K562 | blood: | n/a | n/a |
| 10 | YY1 | chr2:58478594-58478924 | A549 | lung: | n/a | n/a |
| 11 | POLR2A | chr2:58478565-58478725 | GM12878 | blood: | n/a | n/a |
| 12 | POLR2A | chr2:58478486-58478887 | GM12878 | blood: | n/a | n/a |
| 13 | HEY1 | chr2:58478565-58478743 | K562 | blood: | n/a | n/a |
| 14 | POLR2A | chr2:58478552-58478929 | GM12892 | blood: | n/a | n/a |
| 15 | POLR2A | chr2:58478476-58478891 | Gliobla | brain: | n/a | n/a |
| 16 | POLR2A | chr2:58478596-58478883 | GM12878 | blood: | n/a | n/a |
| 17 | POLR2A | chr2:58478549-58478921 | HepG2 | liver: | n/a | n/a |
| 18 | POLR2A | chr2:58478522-58478800 | Hela-S3 | cervix: | n/a | n/a |
| 19 | GABPA | chr2:58478581-58478828 | GM12878 | blood: | n/a | n/a |
| 20 | POLR2A | chr2:58478564-58478852 | A549 | lung: | n/a | n/a |
| 21 | POLR2A | chr2:58478558-58478708 | K562 | blood: | n/a | n/a |
| 22 | POLR2A | chr2:58478598-58478984 | Hela-S3 | cervix: | n/a | n/a |
| 23 | POLR2A | chr2:58478585-58478868 | H1-hESC | embryonic stem cell: | n/a | n/a |
| 24 | POLR2A | chr2:58478493-58478791 | H1-hESC | embryonic stem cell: | n/a | n/a |
| 25 | TAF1 | chr2:58478479-58478920 | H1-hESC | embryonic stem cell: | n/a | n/a |
| 26 | POLR2A | chr2:58478507-58478710 | HUVEC | blood vessel: | n/a | n/a |
| 27 | POLR2A | chr2:58478506-58479271 | H1-hESC | embryonic stem cell: | n/a | n/a |
| 28 | POLR2A | chr2:58478596-58478780 | MCF-7 | breast: | n/a | n/a |
| No data |
| No data |
(count:1 , 50 per page) page:
1
| No. | lncRNA name | Chromosome Location | lncRNA alias |
|---|---|---|---|
| 1 | lnc-FANCL-4 | chr2:58478585-58479810 | NONHSAT070851 |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| EIF3FP3 | TF binding region |
rSNPs within LD-proxies of this variant (count:9)
| rs_ID | r2[population] |
|---|---|
| rs10179025 | 0.85[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs10185542 | 1.00[AMR][1000 genomes] |
| rs10185758 | 1.00[AMR][1000 genomes] |
| rs13409706 | 1.00[AMR][1000 genomes] |
| rs13418777 | 1.00[AMR][1000 genomes] |
| rs13424848 | 0.83[AMR][1000 genomes] |
| rs13428078 | 1.00[AMR][1000 genomes] |
| rs28391566 | 0.85[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs28668929 | 0.80[AFR][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 | nsv999042 | chr2:58326123-58530903 | Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 14 gene(s) | inside rSNPs | diseases |
| 2 | nsv535734 | chr2:58326123-58530903 | ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 14 gene(s) | inside rSNPs | diseases |
| 3 | nsv979006 | chr2:58477513-58480966 | Inactive region | TF binding regionCpG islandChromatin interactive regionlncRNA | 1 gene(s) | inside rSNPs | n/a |
| No data |
Chromatin state (count:0 , 50 per page) page:
| No data |
