Variant report
| Variant | rs12339554 |
|---|---|
| Chromosome Location | chr9:86696287-86696288 |
| 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:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr9:86693838..86695435-chr9:86695774..86698504,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:9)
| rs_ID | r2[population] |
|---|---|
| rs10120996 | 1.00[CEU][hapmap] |
| rs10868094 | 0.84[AMR][1000 genomes] |
| rs12236416 | 0.93[AFR][1000 genomes] |
| rs17086788 | 0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs2118166 | 1.00[CEU][hapmap];0.90[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap] |
| rs59003190 | 0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs72749160 | 0.85[AMR][1000 genomes];0.88[EUR][1000 genomes] |
| rs72749164 | 0.88[AMR][1000 genomes];0.97[EUR][1000 genomes] |
| rs7871328 | 0.82[JPT][hapmap];0.83[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:4 , 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 | nsv831644 | chr9:86534310-86704395 | Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 81 gene(s) | inside rSNPs | diseases |
| 2 | nsv614762 | chr9:86625243-86700593 | Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer | TF binding regionChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
| 3 | nsv1045322 | chr9:86666993-86701912 | Weak transcription Enhancers Bivalent Enhancer | TF binding regionChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
| 4 | nsv893515 | chr9:86693912-86834719 | Weak transcription Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats | Chromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs12339554 | C9orf64 | cis | parietal | SCAN |
| rs12339554 | C9orf64 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr9:86695800-86697800 | Enhancers | Brain Germinal Matrix | brain |
