Variant report
| Variant | rs4660100 |
|---|---|
| Chromosome Location | chr1:241685186-241685187 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:15)
- CpG islands (count:0)
- Chromatin interactive region (count:4)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:15 , 50 per page) page:
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| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | EP300 | chr1:241685048-241685345 | HepG2 | liver: | n/a | n/a |
| 2 | FOXA1 | chr1:241684976-241685356 | HepG2 | liver: | n/a | n/a |
| 3 | FOXA2 | chr1:241684380-241685929 | HepG2 | liver: | n/a | n/a |
| 4 | NFIC | chr1:241684917-241685443 | HepG2 | liver: | n/a | n/a |
| 5 | MYBL2 | chr1:241684928-241685430 | HepG2 | liver: | n/a | n/a |
| 6 | FOXA1 | chr1:241684965-241685904 | HepG2 | liver: | n/a | n/a |
| 7 | HNF4A | chr1:241685073-241685368 | HepG2 | liver: | n/a | chr1:241685133-241685147 chr1:241685132-241685147 chr1:241685138-241685146 |
| 8 | FOXA1 | chr1:241685012-241685441 | HepG2 | liver: | n/a | n/a |
| 9 | TCF7L2 | chr1:241685044-241685481 | HepG2 | liver: | n/a | n/a |
| 10 | GATA3 | chr1:241685164-241685517 | SH-SY5Y | brain: | n/a | n/a |
| 11 | HNF4A | chr1:241685065-241685279 | HepG2 | liver: | n/a | chr1:241685133-241685147 chr1:241685132-241685147 chr1:241685138-241685146 |
| 12 | FOXA2 | chr1:241685063-241685322 | HepG2 | liver: | n/a | n/a |
| 13 | FOXA1 | chr1:241684921-241685924 | HepG2 | liver: | n/a | n/a |
| 14 | ARID3A | chr1:241685036-241685352 | HepG2 | liver: | n/a | n/a |
| 15 | SP1 | chr1:241685019-241685406 | HepG2 | liver: | n/a | n/a |
| No data |
(count:4 , 50 per page) page:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr1:241681125..241684072-chr1:241685116..241687074,3 | MCF-7 | breast: | |
| 2 | chr1:241683433..241685881-chr1:241689141..241691385,3 | MCF-7 | breast: | |
| 3 | chr1:241684656..241686191-chr1:242009808..242012105,2 | K562 | blood: | |
| 4 | chr1:241677220..241680834-chr1:241684726..241688550,4 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| FH | TF binding region |
| ENSG00000174371 | Chromatin interaction |
| ENSG00000091483 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:14)
| rs_ID | r2[population] |
|---|---|
| rs10926507 | 0.86[EUR][1000 genomes] |
| rs12071124 | 0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs12120348 | 0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs1414493 | 0.87[EUR][1000 genomes] |
| rs2153694 | 0.88[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs2994982 | 0.88[EUR][1000 genomes];0.83[ASN][1000 genomes] |
| rs2994985 | 0.88[EUR][1000 genomes];0.85[ASN][1000 genomes] |
| rs2994987 | 0.88[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs2994989 | 0.88[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs4310432 | 0.86[EUR][1000 genomes] |
| rs4659607 | 0.88[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs6678766 | 0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs6679290 | 0.86[EUR][1000 genomes] |
| rs7530270 | 0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv918034 | chr1:241072791-242005532 | Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA | 32 gene(s) | inside rSNPs | diseases |
| 2 | nsv997966 | chr1:241100739-242087629 | Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA | 40 gene(s) | inside rSNPs | diseases |
| 3 | nsv949442 | chr1:241432051-241730054 | Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 11 gene(s) | inside rSNPs | diseases |
| 4 | nsv1002214 | chr1:241458939-242099790 | Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 37 gene(s) | inside rSNPs | diseases |
| 5 | nsv549460 | chr1:241494578-241833287 | Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 27 gene(s) | inside rSNPs | diseases |
| 6 | nsv1009579 | chr1:241499537-241824631 | Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 27 gene(s) | inside rSNPs | diseases |
| 7 | nsv530112 | chr1:241522031-241840269 | Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 25 gene(s) | inside rSNPs | diseases |
| 8 | nsv873368 | chr1:241533392-242195928 | Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 36 gene(s) | inside rSNPs | diseases |
| 9 | nsv873371 | chr1:241667244-241747838 | Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 5 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:241684200-241686200 | Enhancers | Liver | Liver |
| 2 | chr1:241684200-241688400 | Weak transcription | K562 | blood |
| 3 | chr1:241685000-241686000 | Enhancers | HepG2 | liver |
