Variant report
| Variant | rs73873740 |
|---|---|
| Chromosome Location | chr3:156585557-156585558 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:1 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr3:156391139..156393607-chr3:156585246..156587424,3 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000243926 | Chromatin interaction |
| ENSG00000163659 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:18)
| rs_ID | r2[population] |
|---|---|
| rs10513499 | 0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes] |
| rs16826825 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes] |
| rs16826869 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs16826877 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs2101167 | 0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes] |
| rs55687414 | 0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes] |
| rs55726754 | 0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes] |
| rs55928997 | 0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes] |
| rs55951025 | 0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes] |
| rs56126252 | 0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes] |
| rs56413335 | 0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs58158797 | 0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes] |
| rs59229493 | 0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes] |
| rs59870247 | 0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes] |
| rs60204765 | 0.88[AMR][1000 genomes];0.96[EUR][1000 genomes] |
| rs60561257 | 0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes] |
| rs73873745 | 0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes] |
| rs73873746 | 0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][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 | nsv877685 | chr3:156444383-156611676 | Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 48 gene(s) | inside rSNPs | diseases |
| 2 | nsv829765 | chr3:156568263-156718496 | Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 7 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs73873740 | LINC00886 | cis | Thyroid | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr3:156581200-156585600 | Weak transcription | Breast variant Human Mammary Epithelial Cells (vHMEC) | Breast |
