Variant report
| Variant | rs974461 |
|---|---|
| Chromosome Location | chr20:53160657-53160658 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:5)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:5 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr18:58081071..58081577-chr20:53160428..53161007,2 | MCF-7 | breast: | |
| 2 | chr20:53156431..53159299-chr20:53159745..53162526,2 | MCF-7 | breast: | |
| 3 | chr20:53158565..53163438-chr20:53165298..53171299,6 | MCF-7 | breast: | |
| 4 | chr17:56707753..56709458-chr20:53160643..53162668,2 | MCF-7 | breast: | |
| 5 | chr20:53151757..53155024-chr20:53157486..53161432,6 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000212195 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:25)
| rs_ID | r2[population] |
|---|---|
| rs10485786 | 0.96[ASN][1000 genomes] |
| rs16999731 | 0.85[ASN][1000 genomes] |
| rs16999736 | 0.96[ASN][1000 genomes] |
| rs2426521 | 0.81[ASN][1000 genomes] |
| rs2426522 | 0.87[AMR][1000 genomes];0.88[ASN][1000 genomes] |
| rs2426525 | 0.98[ASN][1000 genomes] |
| rs2426526 | 0.96[ASN][1000 genomes] |
| rs2426529 | 0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs2426530 | 0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs2426531 | 0.98[ASN][1000 genomes] |
| rs2426535 | 1.00[ASN][1000 genomes] |
| rs2426536 | 0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs57402636 | 1.00[ASN][1000 genomes] |
| rs6014049 | 0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes] |
| rs6023344 | 0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs6091909 | 0.98[ASN][1000 genomes] |
| rs6098044 | 0.96[ASN][1000 genomes] |
| rs6098064 | 0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs6098074 | 0.87[AMR][1000 genomes];0.86[EUR][1000 genomes] |
| rs726770 | 0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs7272302 | 0.88[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs7274532 | 0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs73276924 | 0.98[ASN][1000 genomes] |
| rs8117905 | 0.82[AMR][1000 genomes];0.86[EUR][1000 genomes] |
| rs8126261 | 0.96[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 | nsv1067497 | chr20:53146241-53751820 | Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 66 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr20:53153000-53161800 | Weak transcription | Osteobl | bone |
| 2 | chr20:53158800-53161200 | Weak transcription | Fetal Brain Male | brain |
