Variant report
| Variant | rs3014824 |
|---|---|
| Chromosome Location | chr1:153401588-153401589 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:17)
- CpG islands (count:0)
- Chromatin interactive region (count:3)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:17 , 50 per page) page:
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| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | ZNF143 | chr1:153401404-153401599 | H1-hESC | embryonic stem cell: | n/a | n/a |
| 2 | CTCF | chr1:153401440-153401590 | HMEC | breast: | n/a | chr1:153401483-153401496 |
| 3 | CTCF | chr1:153401440-153401590 | SAEC | small airway: | n/a | chr1:153401483-153401496 |
| 4 | CTCF | chr1:153401388-153401596 | H1-hESC | embryonic stem cell: | n/a | chr1:153401483-153401496 |
| 5 | CTCF | chr1:153401341-153401628 | K562 | blood: | n/a | chr1:153401483-153401496 |
| 6 | CTCF | chr1:153401460-153401610 | HepG2 | liver: | n/a | chr1:153401483-153401496 |
| 7 | CTCF | chr1:153401500-153401650 | NHEK | skin: | n/a | n/a |
| 8 | RAD21 | chr1:153401369-153401650 | H1-hESC | embryonic stem cell: | n/a | chr1:153401486-153401496 chr1:153401486-153401498 chr1:153401481-153401500 |
| 9 | CTCF | chr1:153401440-153401590 | SK-N-SH_RA | brain: | n/a | chr1:153401483-153401496 |
| 10 | CTCF | chr1:153401310-153401684 | H1-hESC | embryonic stem cell: | n/a | chr1:153401483-153401496 |
| 11 | CTCF | chr1:153401480-153401630 | NHDF-neo | bronchial: | n/a | chr1:153401483-153401496 |
| 12 | CTCF | chr1:153401580-153401730 | HCM | heart: | n/a | n/a |
| 13 | RAD21 | chr1:153401284-153401690 | H1-hESC | embryonic stem cell: | n/a | chr1:153401486-153401496 chr1:153401486-153401498 chr1:153401481-153401500 |
| 14 | CTCF | chr1:153401305-153401611 | H1-hESC | embryonic stem cell: | n/a | chr1:153401483-153401496 |
| 15 | CTCF | chr1:153401460-153401610 | HMF | breast: | n/a | chr1:153401483-153401496 |
| 16 | RAD21 | chr1:153401289-153401628 | H1-hESC | embryonic stem cell: | n/a | chr1:153401486-153401496 chr1:153401486-153401498 chr1:153401481-153401500 |
| 17 | CTCF | chr1:153401380-153401686 | K562 | blood: | n/a | chr1:153401483-153401496 |
| No data |
(count:3 , 50 per page) page:
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| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000203781 | TF binding region |
rSNPs within LD-proxies of this variant (count:11)
| rs_ID | r2[population] |
|---|---|
| rs1998844 | 0.84[ASW][hapmap];0.91[LWK][hapmap];0.87[MKK][hapmap];0.82[YRI][hapmap] |
| rs2986206 | 0.82[YRI][hapmap] |
| rs2986210 | 0.84[ASW][hapmap];0.91[LWK][hapmap];0.87[MKK][hapmap];0.82[YRI][hapmap] |
| rs2986214 | 0.82[YRI][hapmap] |
| rs3006433 | 0.82[YRI][hapmap] |
| rs3006438 | 0.82[YRI][hapmap] |
| rs3014839 | 0.82[YRI][hapmap] |
| rs3014843 | 0.84[ASW][hapmap];0.91[LWK][hapmap];0.87[MKK][hapmap];0.82[YRI][hapmap] |
| rs3014849 | 0.82[YRI][hapmap] |
| rs6587742 | 0.82[YRI][hapmap] |
| rs9633411 | 0.88[MKK][hapmap];0.82[YRI][hapmap] |
Variant overlapped rSNPs/rCNVs (count:5 , 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 | nsv1010488 | chr1:152901263-153670972 | Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 236 gene(s) | inside rSNPs | diseases |
| 2 | nsv535171 | chr1:152901263-153670972 | Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 236 gene(s) | inside rSNPs | diseases |
| 3 | nsv533877 | chr1:152923645-153468131 | Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 56 gene(s) | inside rSNPs | diseases |
| 4 | nsv1002705 | chr1:153307852-153525589 | Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 152 gene(s) | inside rSNPs | diseases |
| 5 | esv3355423 | chr1:153401528-153405726 | Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS | TF binding regionChromatin interactive region | 2 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:5)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs3014824 | LCE1B | cis | cerebellum | SCAN |
| rs3014824 | LCE3D | cis | parietal | SCAN |
| rs3014824 | SPRR4 | cis | parietal | SCAN |
| rs3014824 | S100A7A | cis | cerebellum | SCAN |
| rs3014824 | DENND4B | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:153401400-153403400 | Weak transcription | iPS DF 19.11 Cell Line | embryonic stem cell |
