Variant report
| Variant | rs28460139 |
|---|---|
| Chromosome Location | chr20:52893650-52893651 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:6)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:6 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr20:52892973..52894968-chr20:52956980..52958556,2 | MCF-7 | breast: | |
| 2 | chr20:52892335..52894745-chr20:52921772..52923928,2 | MCF-7 | breast: | |
| 3 | chr20:52891210..52894147-chr20:52899496..52901678,2 | MCF-7 | breast: | |
| 4 | chr20:52891755..52894002-chr3:64171405..64173308,2 | MCF-7 | breast: | |
| 5 | chr20:52891578..52893729-chr20:52943256..52945368,2 | MCF-7 | breast: | |
| 6 | chr20:52891487..52895363-chr20:52902222..52905146,4 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000226017 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:25)
| rs_ID | r2[population] |
|---|---|
| rs1040857 | 0.97[ASN][1000 genomes] |
| rs10485791 | 0.84[ASN][1000 genomes] |
| rs1157418 | 0.89[ASN][1000 genomes] |
| rs1293134 | 0.89[ASN][1000 genomes] |
| rs1343081 | 0.89[ASN][1000 genomes] |
| rs1477734 | 0.89[ASN][1000 genomes] |
| rs1477735 | 0.89[ASN][1000 genomes] |
| rs16999299 | 0.93[ASN][1000 genomes] |
| rs16999320 | 0.89[ASN][1000 genomes] |
| rs16999351 | 0.90[ASN][1000 genomes] |
| rs28372633 | 0.93[ASN][1000 genomes] |
| rs292116 | 0.93[AMR][1000 genomes];0.89[EUR][1000 genomes] |
| rs292142 | 0.87[AMR][1000 genomes];0.90[ASN][1000 genomes] |
| rs4811496 | 0.85[AMR][1000 genomes] |
| rs6013948 | 0.97[ASN][1000 genomes] |
| rs6013954 | 0.89[ASN][1000 genomes] |
| rs6013957 | 0.90[ASN][1000 genomes] |
| rs6023079 | 0.96[AMR][1000 genomes];0.89[EUR][1000 genomes] |
| rs6023086 | 0.93[ASN][1000 genomes] |
| rs6023089 | 0.89[ASN][1000 genomes] |
| rs6023092 | 0.89[ASN][1000 genomes] |
| rs6023096 | 0.90[ASN][1000 genomes] |
| rs6023105 | 0.85[ASN][1000 genomes] |
| rs7266330 | 0.86[ASN][1000 genomes] |
| rs73137452 | 0.96[AMR][1000 genomes];0.86[EUR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:5 , 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 |
| 4 | nsv962638 | chr20:52883415-52917517 | Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS | Chromatin interactive regionlncRNA | 13 gene(s) | inside rSNPs | diseases |
| 5 | nsv178887 | chr20:52885413-52894836 | Enhancers Weak transcription | Chromatin interactive region | 7 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr20:52891800-52893800 | Enhancers | Stomach Mucosa | stomach |
| 2 | chr20:52892800-52894000 | Enhancers | Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells | embryonic stem cell |
| 3 | chr20:52893200-52894000 | Enhancers | H1 BMP4 Derived Trophoblast Cultured Cells | ES cell derived |
