Variant report
| Variant | rs12444890 |
|---|---|
| Chromosome Location | chr16:71636026-71636027 |
| 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 | chr16:71634121..71636611-chr16:71640952..71642935,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:20)
| rs_ID | r2[population] |
|---|---|
| rs10500562 | 1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes] |
| rs12447033 | 0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes] |
| rs12447672 | 0.81[AFR][1000 genomes] |
| rs12922775 | 0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes] |
| rs12923781 | 0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes] |
| rs12924650 | 0.81[AFR][1000 genomes] |
| rs12927768 | 0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes] |
| rs12931191 | 1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes] |
| rs12935422 | 0.97[AFR][1000 genomes];0.87[AMR][1000 genomes] |
| rs17282500 | 1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs17347255 | 0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes] |
| rs17354693 | 0.89[AMR][1000 genomes];0.87[EUR][1000 genomes] |
| rs17356206 | 0.81[AFR][1000 genomes] |
| rs34181942 | 0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes] |
| rs34381861 | 0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs34753286 | 0.84[AMR][1000 genomes];0.86[EUR][1000 genomes] |
| rs35538253 | 0.97[AFR][1000 genomes] |
| rs71403859 | 0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs7203606 | 0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes] |
| rs8063455 | 0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][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 | esv3347477 | chr16:71555148-71985177 | Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 56 gene(s) | inside rSNPs | diseases |
| 2 | nsv1063338 | chr16:71612346-71752968 | Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 16 gene(s) | inside rSNPs | diseases |
| 3 | esv3430225 | chr16:71633500-71661205 | Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 11 gene(s) | inside rSNPs | diseases |
| 4 | esv3339539 | chr16:71635901-71639399 | Weak transcription | Chromatin interactive region | n/a | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs12444890 | RP11-432I5.1 | cis | Thyroid | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr16:71635200-71640600 | Weak transcription | HepG2 | liver |
