Variant report
| Variant | rs4734291 |
|---|---|
| Chromosome Location | chr8:95820594-95820595 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:1)
- CpG islands (count:0)
- Chromatin interactive region (count:5)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:1 , 50 per page) page:
1
| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | TCF12 | chr8:95820176-95820612 | SK-N-SH | brain: | n/a | chr8:95820431-95820440 |
| No data |
(count:5 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr8:95815705..95817317-chr8:95819683..95821432,2 | K562 | blood: | |
| 2 | chr8:95730308..95733697-chr8:95819325..95823735,5 | MCF-7 | breast: | |
| 3 | chr8:95729949..95733435-chr8:95819627..95822552,3 | MCF-7 | breast: | |
| 4 | chr8:95809644..95812311-chr8:95818366..95820931,2 | K562 | blood: | |
| 5 | chr8:95819563..95823488-chr8:95834071..95836286,3 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| INTS8 | TF binding region |
| ENSG00000156162 | Chromatin interaction |
| ENSG00000164941 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:46)
| rs_ID | r2[population] |
|---|---|
| rs10098778 | 0.83[JPT][hapmap] |
| rs10099941 | 0.82[JPT][hapmap] |
| rs10112232 | 0.83[GIH][hapmap] |
| rs10441538 | 0.83[GIH][hapmap] |
| rs10956928 | 0.81[JPT][hapmap] |
| rs10956929 | 0.87[JPT][hapmap] |
| rs10956930 | 0.87[JPT][hapmap] |
| rs10956931 | 0.87[JPT][hapmap] |
| rs10956932 | 0.87[JPT][hapmap] |
| rs12545596 | 0.87[JPT][hapmap] |
| rs12548999 | 0.87[JPT][hapmap] |
| rs12679044 | 1.00[JPT][hapmap] |
| rs13255935 | 0.83[JPT][hapmap] |
| rs13257021 | 0.83[JPT][hapmap] |
| rs13271644 | 0.83[GIH][hapmap] |
| rs1453377 | 0.83[JPT][hapmap] |
| rs16893776 | 0.83[JPT][hapmap] |
| rs2123647 | 0.87[JPT][hapmap] |
| rs2945554 | 0.87[JPT][hapmap] |
| rs2956216 | 0.87[JPT][hapmap] |
| rs3019175 | 0.81[JPT][hapmap] |
| rs4735328 | 0.87[JPT][hapmap] |
| rs4735331 | 0.87[JPT][hapmap] |
| rs4735332 | 0.87[JPT][hapmap] |
| rs4735336 | 0.83[JPT][hapmap] |
| rs4735337 | 0.83[JPT][hapmap] |
| rs4735339 | 0.88[JPT][hapmap] |
| rs477653 | 0.86[JPT][hapmap] |
| rs550418 | 0.87[JPT][hapmap] |
| rs550564 | 0.87[JPT][hapmap] |
| rs551270 | 0.87[JPT][hapmap] |
| rs6471499 | 0.87[JPT][hapmap] |
| rs6471500 | 0.87[JPT][hapmap] |
| rs6471503 | 0.83[JPT][hapmap] |
| rs683832 | 0.87[JPT][hapmap] |
| rs6982393 | 0.83[JPT][hapmap] |
| rs6983000 | 0.87[JPT][hapmap] |
| rs6987256 | 0.87[JPT][hapmap] |
| rs7001535 | 0.87[JPT][hapmap] |
| rs7005317 | 0.87[JPT][hapmap] |
| rs7015841 | 0.87[JPT][hapmap] |
| rs7017487 | 0.87[JPT][hapmap] |
| rs713113 | 0.83[GIH][hapmap] |
| rs726816 | 0.83[JPT][hapmap] |
| rs7820818 | 0.87[JPT][hapmap] |
| rs7845219 | 0.88[CHD][hapmap];1.00[JPT][hapmap] |
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 | nsv1017301 | chr8:95273503-96248352 | Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 87 gene(s) | inside rSNPs | diseases |
| 2 | nsv539680 | chr8:95273503-96248352 | Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 87 gene(s) | inside rSNPs | diseases |
| 3 | nsv532338 | chr8:95296118-95971825 | Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 61 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:5)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs4734291 | PLEKHF2 | cis | parietal | SCAN |
| rs4734291 | SHBG | trans | cerebellum | SCAN |
| rs4734291 | TP53INP1 | cis | Esophagus Muscularis | GTEx |
| rs4734291 | RBM12B | cis | cerebellum | SCAN |
| rs4734291 | TP53INP1 | Cis_1M | lymphoblastoid | RTeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr8:95815800-95826600 | Weak transcription | Pancreatic Islets | Pancreatic Islet |
| 2 | chr8:95817400-95820800 | Weak transcription | H1 BMP4 Derived Mesendoderm Cultured Cells | ES cell derived |
| 3 | chr8:95818000-95824400 | Weak transcription | Fetal Intestine Small | intestine |
| 4 | chr8:95819600-95821000 | Enhancers | IMR90 fetal lung fibroblasts Cell Line | lung |
| 5 | chr8:95819800-95822600 | Weak transcription | K562 | blood |
