Variant report
| Variant | rs6878565 |
|---|---|
| Chromosome Location | chr5:52564204-52564205 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
| No data |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:21)
| rs_ID | r2[population] |
|---|---|
| rs10040078 | 0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs10040441 | 0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes] |
| rs10043976 | 0.81[AFR][1000 genomes] |
| rs10059098 | 0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes] |
| rs10076999 | 0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes] |
| rs10079630 | 0.81[AFR][1000 genomes] |
| rs13354542 | 0.84[AFR][1000 genomes] |
| rs13360056 | 0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes] |
| rs1374056 | 0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs16881207 | 0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs16881273 | 0.83[AFR][1000 genomes] |
| rs16881297 | 0.81[AFR][1000 genomes] |
| rs28461700 | 0.81[AFR][1000 genomes] |
| rs4260626 | 0.83[AFR][1000 genomes] |
| rs4264908 | 0.83[AFR][1000 genomes] |
| rs56913728 | 0.84[AFR][1000 genomes];0.83[ASN][1000 genomes] |
| rs59109818 | 0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs6869330 | 0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes] |
| rs6883267 | 0.83[AFR][1000 genomes] |
| rs6886254 | 0.83[AFR][1000 genomes] |
| rs7710631 | 0.83[AFR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv949005 | chr5:52188028-52808229 | Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 35 gene(s) | inside rSNPs | diseases |
| 2 | esv2752745 | chr5:52422063-53343529 | Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 22 gene(s) | inside rSNPs | diseases |
| 3 | nsv830297 | chr5:52492494-52707758 | Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
| 4 | nsv522454 | chr5:52492677-52571758 | Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr5:52563400-52564400 | ZNF genes & repeats | hESC Derived CD184+ Endoderm Cultured Cells | ES cell derived |
| 2 | chr5:52563800-52575200 | Weak transcription | Breast variant Human Mammary Epithelial Cells (vHMEC) | Breast |
