Variant report
| Variant | rs6506940 |
|---|---|
| Chromosome Location | chr18:29333635-29333636 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:1 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr18:29333142..29335826-chr3:113464597..113467025,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000242659 | Chromatin interaction |
| ENSG00000114573 | Chromatin interaction |
| ENSG00000121579 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:20)
| rs_ID | r2[population] |
|---|---|
| rs1482515 | 1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs1482518 | 0.90[AMR][1000 genomes];0.86[EUR][1000 genomes] |
| rs1842785 | 0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes] |
| rs1905159 | 0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs3912315 | 0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes] |
| rs4239369 | 0.97[ASN][1000 genomes] |
| rs4308024 | 0.97[ASN][1000 genomes] |
| rs4308025 | 0.97[ASN][1000 genomes] |
| rs4308026 | 0.97[ASN][1000 genomes] |
| rs4799316 | 0.97[ASN][1000 genomes] |
| rs4799318 | 1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs4799595 | 0.92[ASN][1000 genomes] |
| rs4799601 | 0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs594334 | 0.82[AMR][1000 genomes] |
| rs7233853 | 0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes] |
| rs7234679 | 0.97[ASN][1000 genomes] |
| rs8082962 | 0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs8085381 | 0.84[EUR][1000 genomes] |
| rs966287 | 0.92[ASN][1000 genomes] |
| rs9783847 | 0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.90[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 | nsv1059078 | chr18:29225522-29454980 | Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 22 gene(s) | inside rSNPs | diseases |
| 2 | nsv543675 | chr18:29225522-29454980 | Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 22 gene(s) | inside rSNPs | diseases |
| 3 | nsv431975 | chr18:29311034-29527902 | Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 26 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs6506940 | AQP4 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr18:29321400-29353800 | Weak transcription | Liver | Liver |
