Variant report
| Variant | rs2903466 |
|---|---|
| Chromosome Location | chr20:40816877-40816878 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:4)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:4 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr20:40814588..40817431-chr20:55821532..55823212,2 | MCF-7 | breast: | |
| 2 | chr20:40814293..40823247-chr20:55839406..55843117,11 | MCF-7 | breast: | |
| 3 | chr20:40814621..40823038-chr20:55816699..55826328,24 | MCF-7 | breast: | |
| 4 | chr20:40814194..40820510-chr20:55816660..55821393,15 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000226308 | Chromatin interaction |
| ENSG00000101144 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:19)
| rs_ID | r2[population] |
|---|---|
| rs17221067 | 0.85[CHD][hapmap] |
| rs17221137 | 0.85[CHD][hapmap] |
| rs17221326 | 0.86[TSI][hapmap] |
| rs17221823 | 0.85[CEU][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes] |
| rs17312515 | 0.85[CHD][hapmap] |
| rs55789113 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs55796708 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs55889296 | 0.96[AMR][1000 genomes];0.91[EUR][1000 genomes] |
| rs56039253 | 0.85[AMR][1000 genomes];0.89[EUR][1000 genomes] |
| rs56256174 | 0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes] |
| rs56344866 | 0.89[AMR][1000 genomes];0.89[EUR][1000 genomes] |
| rs6016698 | 0.85[CHD][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap] |
| rs6030014 | 0.85[CHD][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap] |
| rs6102693 | 0.85[MEX][hapmap] |
| rs6513775 | 1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap] |
| rs73118438 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs73120412 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs73120420 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs73120444 | 0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | esv2751913 | chr20:40422982-41269321 | Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 22 gene(s) | inside rSNPs | diseases |
| 2 | nsv532516 | chr20:40451059-41097155 | Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 18 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs2903466 | KCNS1 | cis | parietal | SCAN |
| rs2903466 | CTNNBL1 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr20:40805000-40820400 | Weak transcription | Breast Myoepithelial Primary Cells | Breast |
| 2 | chr20:40816600-40817400 | Enhancers | Pancreatic Islets | Pancreatic Islet |
