Variant report
| Variant | rs11716981 |
|---|---|
| Chromosome Location | chr3:147083388-147083389 |
| allele | C/T |
| 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 | chr3:147080801..147083762-chr3:147109705..147112300,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000152977 | Chromatin interaction |
| ENSG00000174963 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:15)
| rs_ID | r2[population] |
|---|---|
| rs11720889 | 0.88[CEU][hapmap];0.90[TSI][hapmap] |
| rs13067005 | 0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs13079809 | 0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs13085221 | 1.00[CHB][hapmap];1.00[JPT][hapmap] |
| rs13085931 | 0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs1503731 | 0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs17507918 | 0.81[AMR][1000 genomes];0.95[ASN][1000 genomes] |
| rs17567193 | 0.95[ASN][1000 genomes] |
| rs2062599 | 0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs35716200 | 0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs4368473 | 0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap] |
| rs66483436 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs67690801 | 0.81[AMR][1000 genomes];0.95[ASN][1000 genomes] |
| rs73166642 | 0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs73166647 | 0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page:
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| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1013080 | chr3:147008962-147167690 | Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 7 gene(s) | inside rSNPs | diseases |
| 2 | nsv536763 | chr3:147008962-147167690 | Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 7 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs11716981 | ZIC4 | cis | cerebellum | SCAN |
| rs11716981 | MBNL1 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr3:147077600-147083400 | Weak transcription | H1 Derived Neuronal Progenitor Cultured Cells | ES cell derived |
