Variant report
| Variant | rs475612 |
|---|---|
| Chromosome Location | chr2:169776746-169776747 |
| 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 | chr2:169775702..169778963-chr2:169780525..169783462,3 | K562 | blood: | |
| 2 | chr2:169775702..169778664-chr2:169780525..169782299,2 | K562 | blood: | |
| 3 | chr2:169769700..169774524-chr2:169775649..169779398,6 | K562 | blood: | |
| 4 | chr2:169627058..169629094-chr2:169775848..169778213,2 | K562 | blood: | |
| 5 | chr2:169629191..169630841-chr2:169776722..169777731,4 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000152253 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:20)
| rs_ID | r2[population] |
|---|---|
| rs484066 | 0.84[EUR][1000 genomes] |
| rs485094 | 0.91[EUR][1000 genomes] |
| rs486981 | 0.91[EUR][1000 genomes] |
| rs494874 | 0.89[EUR][1000 genomes] |
| rs502570 | 0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs504979 | 0.85[EUR][1000 genomes] |
| rs508506 | 0.90[EUR][1000 genomes] |
| rs518598 | 0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs537183 | 0.98[EUR][1000 genomes] |
| rs552976 | 0.90[EUR][1000 genomes] |
| rs557462 | 0.81[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs563694 | 0.98[EUR][1000 genomes] |
| rs566879 | 0.91[EUR][1000 genomes] |
| rs569805 | 0.91[EUR][1000 genomes] |
| rs569829 | 0.90[EUR][1000 genomes] |
| rs578763 | 0.94[AMR][1000 genomes];0.92[EUR][1000 genomes] |
| rs579060 | 0.91[EUR][1000 genomes] |
| rs580670 | 0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs853787 | 0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes] |
| rs853789 | 0.96[CEU][hapmap];0.85[EUR][1000 genomes] |
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 | nsv583599 | chr2:169664227-169903096 | Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 12 gene(s) | inside rSNPs | diseases |
| 2 | nsv459943 | chr2:169756930-169799010 | Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers | TF binding regionCpG islandChromatin interactive regionmiRNA target site | 4 gene(s) | inside rSNPs | diseases |
| 3 | nsv583600 | chr2:169756930-169799010 | Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers | TF binding regionCpG islandChromatin interactive regionmiRNA target site | 4 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs475612 | DYNC1I2 | cis | parietal | SCAN |
| rs475612 | C10orf95 | trans | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr2:169770600-169778600 | Weak transcription | Liver | Liver |
