Variant report
| Variant | rs1293142 |
|---|---|
| Chromosome Location | chr20:52918677-52918678 |
| allele | C/T |
| 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:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr20:52916826..52918729-chr3:64490949..64493940,2 | MCF-7 | breast: | |
| 2 | chr20:52917863..52920685-chr20:52931179..52933148,2 | MCF-7 | breast: | |
| 3 | chr20:52908727..52910556-chr20:52917946..52923275,4 | MCF-7 | breast: | |
| 4 | chr1:149223470..149225076-chr20:52916629..52918756,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000206737 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:13)
| rs_ID | r2[population] |
|---|---|
| rs1293143 | 0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs1293144 | 0.83[EUR][1000 genomes] |
| rs1343080 | 0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs1382010 | 0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs1418924 | 0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs1542522 | 0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs2153964 | 0.81[EUR][1000 genomes] |
| rs2153965 | 0.81[EUR][1000 genomes] |
| rs2616335 | 0.81[EUR][1000 genomes] |
| rs2870320 | 0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs6091849 | 0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs6097895 | 0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs6097896 | 0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][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 | nsv586224 | chr20:52474850-53279490 | Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 338 gene(s) | inside rSNPs | diseases |
| 2 | nsv834010 | chr20:52759824-52932939 | Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 119 gene(s) | inside rSNPs | diseases |
| 3 | nsv834011 | chr20:52858341-53086042 | Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS | Chromatin interactive regionlncRNA | 55 gene(s) | inside rSNPs | diseases |
| No data |
Chromatin state (count:0 , 50 per page) page:
| No data |
