Variant report
| Variant | rs847328 |
|---|---|
| Chromosome Location | chr14:72831006-72831007 |
| allele | C/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 | chr14:72829562..72831650-chr14:72833232..72835996,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:24)
| rs_ID | r2[population] |
|---|---|
| rs10136263 | 0.94[CHD][hapmap];0.89[GIH][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs10141305 | 0.89[ASN][1000 genomes] |
| rs10149207 | 1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[ASN][1000 genomes] |
| rs1072165 | 1.00[ASN][1000 genomes] |
| rs11620677 | 0.86[GIH][hapmap] |
| rs2139596 | 1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[ASN][1000 genomes] |
| rs2190509 | 1.00[CHB][hapmap];1.00[ASN][1000 genomes] |
| rs2529458 | 0.87[ASN][1000 genomes] |
| rs2529459 | 1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes] |
| rs2529465 | 0.87[ASN][1000 genomes] |
| rs2681724 | 0.84[AMR][1000 genomes];1.00[ASN][1000 genomes] |
| rs2681740 | 0.83[CEU][hapmap] |
| rs2681750 | 1.00[CHB][hapmap];1.00[ASN][1000 genomes] |
| rs2681756 | 1.00[ASN][1000 genomes] |
| rs2681758 | 0.87[ASN][1000 genomes] |
| rs2681760 | 0.87[ASN][1000 genomes] |
| rs2681763 | 0.87[ASN][1000 genomes] |
| rs769148 | 1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs8018733 | 0.86[CEU][hapmap] |
| rs847325 | 1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs847329 | 1.00[CHB][hapmap];1.00[JPT][hapmap] |
| rs847330 | 1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes] |
| rs847331 | 1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes] |
| rs847334 | 1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[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 | nsv530794 | chr14:72113818-73034008 | Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA | 8 gene(s) | inside rSNPs | diseases |
| 2 | nsv948800 | chr14:72462557-73150701 | Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA | 11 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:3)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs847328 | TMED10 | cis | parietal | SCAN |
| rs847328 | DPF3 | cis | cerebellum | SCAN |
| rs847328 | C14orf43 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr14:72828000-72831600 | Strong transcription | Cortex derived primary cultured neurospheres | brain |
| 2 | chr14:72829600-72834400 | Weak transcription | Ganglion Eminence derived primary cultured neurospheres | brain |
