Variant report
| Variant | rs10408479 |
|---|---|
| Chromosome Location | chr19:38725032-38725033 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:8)
- CpG islands (count:0)
- Chromatin interactive region (count:17)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:8 , 50 per page) page:
1
| No data |
(count:17 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr19:38723024..38725443-chr19:38878672..38880879,2 | MCF-7 | breast: | |
| 2 | chr19:38717093..38718677-chr19:38724126..38726976,2 | K562 | blood: | |
| 3 | chr19:38724585..38727174-chr19:38883492..38886224,2 | K562 | blood: | |
| 4 | chr19:38723368..38726031-chr19:38797487..38799175,2 | MCF-7 | breast: | |
| 5 | chr19:38724234..38725570-chr19:38893025..38893769,4 | K562 | blood: | |
| 6 | chr19:38723198..38725362-chr19:38864157..38865784,2 | K562 | blood: | |
| 7 | chr19:38724422..38725057-chr19:38864812..38865588,2 | K562 | blood: | |
| 8 | chr19:38720592..38722293-chr19:38724613..38726835,2 | MCF-7 | breast: | |
| 9 | chr19:38723491..38725548-chr19:38807172..38810073,2 | MCF-7 | breast: | |
| 10 | chr19:38724122..38725097-chr19:38877454..38878445,2 | K562 | blood: | |
| 11 | chr19:38724477..38726167-chr19:38793012..38795957,2 | MCF-7 | breast: | |
| 12 | chr19:38724232..38725096-chr19:38825912..38826777,3 | MCF-7 | breast: | |
| 13 | chr19:38724017..38726081-chr19:38800936..38802503,2 | MCF-7 | breast: | |
| 14 | chr19:38724284..38725892-chr19:38729900..38732787,2 | MCF-7 | breast: | |
| 15 | chr19:38716917..38718796-chr19:38722935..38725683,2 | MCF-7 | breast: | |
| 16 | chr19:38724056..38725147-chr19:38825813..38826799,6 | K562 | blood: | |
| 17 | chr19:38723954..38725117-chr19:38825843..38827182,6 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| DPF1 | TF binding region |
| ENSG00000179168 | Chromatin interaction |
| ENSG00000167644 | Chromatin interaction |
| ENSG00000188766 | Chromatin interaction |
| ENSG00000167645 | Chromatin interaction |
| ENSG00000099338 | Chromatin interaction |
| ENSG00000099341 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:42)
| rs_ID | r2[population] |
|---|---|
| rs10401829 | 1.00[AMR][1000 genomes] |
| rs10401835 | 1.00[AMR][1000 genomes] |
| rs10402883 | 1.00[AMR][1000 genomes] |
| rs10403809 | 1.00[AMR][1000 genomes] |
| rs10405381 | 1.00[AMR][1000 genomes] |
| rs10406765 | 1.00[AMR][1000 genomes] |
| rs10407169 | 1.00[AMR][1000 genomes] |
| rs10407230 | 1.00[AMR][1000 genomes] |
| rs10408909 | 1.00[AMR][1000 genomes] |
| rs10412116 | 0.85[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs10413138 | 1.00[AMR][1000 genomes] |
| rs10413363 | 0.85[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs10413551 | 1.00[AMR][1000 genomes] |
| rs10413596 | 1.00[AMR][1000 genomes] |
| rs10414916 | 1.00[AMR][1000 genomes] |
| rs10414927 | 1.00[AMR][1000 genomes] |
| rs10415809 | 1.00[AMR][1000 genomes] |
| rs10421241 | 1.00[AMR][1000 genomes] |
| rs10423429 | 1.00[AMR][1000 genomes] |
| rs10424104 | 1.00[AMR][1000 genomes] |
| rs10424818 | 1.00[AMR][1000 genomes] |
| rs10425099 | 1.00[AMR][1000 genomes] |
| rs10425571 | 1.00[AMR][1000 genomes] |
| rs10426292 | 1.00[AMR][1000 genomes] |
| rs10426458 | 0.85[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs28376501 | 1.00[AMR][1000 genomes] |
| rs28380555 | 1.00[AMR][1000 genomes] |
| rs28421402 | 1.00[AMR][1000 genomes] |
| rs28627637 | 1.00[AMR][1000 genomes] |
| rs28637743 | 1.00[AMR][1000 genomes] |
| rs28649033 | 1.00[AMR][1000 genomes] |
| rs28660098 | 1.00[AMR][1000 genomes] |
| rs28700884 | 1.00[AMR][1000 genomes] |
| rs56134404 | 1.00[AMR][1000 genomes] |
| rs56216562 | 1.00[AMR][1000 genomes] |
| rs58260561 | 1.00[AMR][1000 genomes] |
| rs59571293 | 1.00[AMR][1000 genomes] |
| rs61456950 | 1.00[AMR][1000 genomes] |
| rs71354969 | 1.00[AMR][1000 genomes] |
| rs73630898 | 1.00[AMR][1000 genomes] |
| rs73632925 | 1.00[AMR][1000 genomes] |
| rs73930357 | 1.00[AMR][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 | nsv949296 | chr19:38034722-38763140 | Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 58 gene(s) | inside rSNPs | diseases |
| 2 | nsv833821 | chr19:38629937-38756792 | Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 23 gene(s) | inside rSNPs | diseases |
| 3 | nsv911657 | chr19:38655449-38753786 | Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 20 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr19:38720600-38740400 | Weak transcription | Right Atrium | heart |
| 2 | chr19:38721000-38734400 | Weak transcription | Brain Cingulate Gyrus | brain |
| 3 | chr19:38724200-38734400 | Weak transcription | Foreskin Melanocyte Primary Cells skin01 | Skin |
| 4 | chr19:38725000-38725800 | Weak transcription | Foreskin Fibroblast Primary Cells skin02 | Skin |
| 5 | chr19:38725000-38734400 | Weak transcription | Breast Myoepithelial Primary Cells | Breast |
| 6 | chr19:38725000-38734400 | Weak transcription | A549 | lung |
