Variant report
| Variant | rs4233342 |
|---|---|
| Chromosome Location | chr1:168543445-168543446 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:12)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:12 , 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 | chr1:168543359-168543854 | SK-N-SH | brain: | n/a | n/a |
| 2 | CEBPB | chr1:168543357-168543865 | K562 | blood: | n/a | chr1:168543617-168543628 |
| 3 | GATA1 | chr1:168543391-168543687 | PBDE | blood: | n/a | n/a |
| 4 | RAD21 | chr1:168543439-168543804 | HepG2 | liver: | n/a | n/a |
| 5 | SMC3 | chr1:168543384-168543852 | SK-N-SH | brain: | n/a | n/a |
| 6 | RAD21 | chr1:168543413-168543850 | SK-N-SH | brain: | n/a | n/a |
| 7 | CEBPB | chr1:168543368-168543720 | MCF-7 | breast: | n/a | chr1:168543617-168543628 |
| 8 | RAD21 | chr1:168543415-168543739 | A549 | lung: | n/a | n/a |
| 9 | TEAD4 | chr1:168543430-168543930 | HepG2 | liver: | n/a | n/a |
| 10 | CEBPB | chr1:168543413-168543733 | A549 | lung: | n/a | chr1:168543617-168543628 |
| 11 | CTCF | chr1:168543366-168543981 | A549 | lung: | n/a | n/a |
| 12 | CTCF | chr1:168542949-168543858 | A549 | lung: | n/a | n/a |
| No data |
(count:1 , 50 per page) page:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr1:168408738..168409696-chr1:168543083..168544145,4 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| XCL1 | TF binding region |
rSNPs within LD-proxies of this variant (count:18)
| rs_ID | r2[population] |
|---|---|
| rs10800359 | 0.91[ASN][1000 genomes] |
| rs11801718 | 0.85[ASN][1000 genomes] |
| rs12029370 | 0.82[ASN][1000 genomes] |
| rs12039757 | 0.93[ASN][1000 genomes] |
| rs16860907 | 0.91[ASN][1000 genomes] |
| rs1933099 | 0.91[ASN][1000 genomes] |
| rs2143310 | 0.93[ASN][1000 genomes] |
| rs2143311 | 0.93[ASN][1000 genomes] |
| rs2223584 | 0.80[ASN][1000 genomes] |
| rs2419114 | 0.92[ASN][1000 genomes] |
| rs34038445 | 0.94[ASN][1000 genomes] |
| rs3753938 | 0.94[ASN][1000 genomes] |
| rs4656155 | 0.93[ASN][1000 genomes] |
| rs470739 | 0.81[ASN][1000 genomes] |
| rs7354947 | 0.93[ASN][1000 genomes] |
| rs7532420 | 0.93[ASN][1000 genomes] |
| rs7541604 | 0.81[ASN][1000 genomes] |
| rs7541693 | 0.89[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1014626 | chr1:168441288-168642731 | Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 12 gene(s) | inside rSNPs | diseases |
| 2 | nsv535196 | chr1:168441288-168642731 | Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 12 gene(s) | inside rSNPs | diseases |
| 3 | nsv1011821 | chr1:168441488-168642592 | Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 12 gene(s) | inside rSNPs | diseases |
| 4 | nsv535197 | chr1:168441488-168642592 | Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 12 gene(s) | inside rSNPs | diseases |
| 5 | nsv1008852 | chr1:168449940-168643905 | Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 12 gene(s) | inside rSNPs | diseases |
| 6 | nsv535198 | chr1:168449940-168643905 | Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 12 gene(s) | inside rSNPs | diseases |
| 7 | nsv1007846 | chr1:168449940-168687265 | Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 12 gene(s) | inside rSNPs | diseases |
| 8 | nsv869415 | chr1:168467284-169153863 | Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 44 gene(s) | inside rSNPs | diseases |
| 9 | esv1792733 | chr1:168526394-168544716 | Enhancers Weak transcription Flanking Active TSS Active TSS | TF binding regionCpG islandChromatin interactive region | 2 gene(s) | inside rSNPs | diseases |
| 10 | nsv831836 | chr1:168538779-168716956 | Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 7 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:168539400-168550600 | Weak transcription | HepG2 | liver |
| 2 | chr1:168543200-168543600 | Enhancers | Primary T helper naive cells from peripheral blood | blood |
| 3 | chr1:168543400-168544200 | Enhancers | Primary T helper memory cells from peripheral blood 1 | blood |
