Variant report
| Variant | rs6127146 |
|---|---|
| Chromosome Location | chr20:52852414-52852415 |
| allele | C/T |
| 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 | chr20:52850887..52853833-chr20:52876658..52879639,2 | MCF-7 | breast: | |
| 2 | chr20:52843581..52850062-chr20:52850195..52855343,9 | MCF-7 | breast: | |
| 3 | chr20:52852339..52854018-chr20:53262598..53264931,2 | MCF-7 | breast: | |
| 4 | chr20:52851637..52853511-chr20:52855095..52857097,2 | MCF-7 | breast: | |
| 5 | chr20:52852394..52854365-chr20:53090904..53092475,2 | MCF-7 | breast: | |
| 6 | chr20:52852335..52854423-chr20:53245467..53248244,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000101134 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:17)
| rs_ID | r2[population] |
|---|---|
| rs10485794 | 1.00[CEU][hapmap] |
| rs11698157 | 0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs1382007 | 0.94[ASN][1000 genomes] |
| rs16999283 | 1.00[CEU][hapmap] |
| rs16999288 | 1.00[CEU][hapmap] |
| rs16999291 | 1.00[CEU][hapmap] |
| rs292112 | 0.93[ASN][1000 genomes] |
| rs292116 | 0.89[EUR][1000 genomes] |
| rs3787559 | 0.80[ASN][1000 genomes] |
| rs41428148 | 1.00[CEU][hapmap] |
| rs4811496 | 0.92[AMR][1000 genomes];0.97[EUR][1000 genomes] |
| rs6013926 | 0.80[ASN][1000 genomes] |
| rs6013927 | 0.80[ASN][1000 genomes] |
| rs6023079 | 0.82[AMR][1000 genomes];0.83[EUR][1000 genomes] |
| rs73137406 | 0.82[ASN][1000 genomes] |
| rs73137452 | 0.82[AMR][1000 genomes];0.81[EUR][1000 genomes] |
| rs986709 | 1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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 | 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 |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr20:52849400-52852800 | Weak transcription | H1 BMP4 Derived Trophoblast Cultured Cells | ES cell derived |
