Variant report
| Variant | rs4233885 |
|---|---|
| Chromosome Location | chr2:10841354-10841355 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:5)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:5 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr2:10836934..10838569-chr2:10840919..10843106,2 | K562 | blood: | |
| 2 | chr2:10839405..10841919-chr2:10851119..10853267,3 | K562 | blood: | |
| 3 | chr2:10841033..10842892-chr2:10910211..10912703,2 | MCF-7 | breast: | |
| 4 | chr2:10828574..10833568-chr2:10841193..10850887,9 | MCF-7 | breast: | |
| 5 | chr2:10830020..10832470-chr2:10841337..10843222,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000243819 | Chromatin interaction |
| ENSG00000115761 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:15)
| rs_ID | r2[population] |
|---|---|
| rs10178212 | 0.80[EUR][1000 genomes] |
| rs10929676 | 0.87[CHB][hapmap] |
| rs10929693 | 0.94[CHB][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap] |
| rs11695330 | 0.83[CEU][hapmap];0.83[EUR][1000 genomes] |
| rs13396733 | 0.81[CHB][hapmap];0.82[JPT][hapmap] |
| rs13403486 | 0.94[CHB][hapmap] |
| rs2357656 | 0.90[TSI][hapmap] |
| rs4586606 | 0.83[EUR][1000 genomes] |
| rs4614910 | 0.83[CEU][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes] |
| rs4669606 | 0.83[CEU][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes] |
| rs4669607 | 0.83[EUR][1000 genomes] |
| rs62127228 | 0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs62127230 | 0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs7593172 | 0.83[EUR][1000 genomes] |
| rs881572 | 0.94[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap] |
Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1000953 | chr2:10717304-10921805 | Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 21 gene(s) | inside rSNPs | diseases |
| 2 | nsv535584 | chr2:10717304-10921805 | Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 21 gene(s) | inside rSNPs | diseases |
| 3 | nsv833381 | chr2:10723465-10911284 | Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 21 gene(s) | inside rSNPs | diseases |
| 4 | nsv1000731 | chr2:10758657-10943882 | Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 20 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs4233885 | CYS1 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr2:10841200-10841600 | Enhancers | ES-I3 Cell Line | embryonic stem cell |
| 2 | chr2:10841200-10841600 | Enhancers | H1 BMP4 Derived Trophoblast Cultured Cells | ES cell derived |
