Variant report
| Variant | rs2705143 |
|---|---|
| Chromosome Location | chr12:48919793-48919794 |
| 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 | chr12:48917515..48920061-chr12:49210634..49213027,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000167535 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:10)
| rs_ID | r2[population] |
|---|---|
| rs10747550 | 0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs10783262 | 0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs11168624 | 0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs2468351 | 0.91[AMR][1000 genomes];0.88[EUR][1000 genomes] |
| rs2705134 | 0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes] |
| rs2705156 | 0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs2731078 | 0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs2731079 | 0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs2956465 | 0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes] |
| rs4492859 | 0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[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 | nsv427911 | chr12:48670336-48979396 | Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 35 gene(s) | inside rSNPs | diseases |
| 2 | esv1803653 | chr12:48905575-48923774 | Weak transcription Active TSS ZNF genes & repeats Enhancers | TF binding regionCpG islandChromatin interactive region | 3 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs2705143 | C12orf54 | cis | Esophagus Mucosa | GTEx |
| rs2705143 | C12orf54 | cis | multi-tissue | Pritchard |
Chromatin state (count:0 , 50 per page) page:
| No data |
