Variant report
| Variant | rs953199 |
|---|---|
| Chromosome Location | chr9:100482976-100482977 |
| allele | G/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:6)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:6 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr9:100477106..100478683-chr9:100480479..100483251,2 | MCF-7 | breast: | |
| 2 | chr9:100458306..100461038-chr9:100482799..100485082,2 | MCF-7 | breast: | |
| 3 | chr9:100480674..100483581-chr9:100484932..100487285,2 | K562 | blood: | |
| 4 | chr9:100476626..100478474-chr9:100481765..100484991,3 | MCF-7 | breast: | |
| 5 | chr9:100471241..100474154-chr9:100481493..100483041,2 | K562 | blood: | |
| 6 | chr9:100481943..100484213-chr9:100684517..100686414,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000136936 | Chromatin interaction |
| ENSG00000136932 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:13)
| rs_ID | r2[population] |
|---|---|
| rs10817988 | 0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs10983513 | 0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs10983546 | 0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs11792527 | 1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs12375515 | 0.98[ASN][1000 genomes] |
| rs1355599 | 0.82[ASN][1000 genomes] |
| rs16923900 | 0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs2805827 | 0.81[ASN][1000 genomes] |
| rs2808672 | 0.86[CHB][hapmap];0.80[CHD][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes] |
| rs2808679 | 0.82[ASN][1000 genomes] |
| rs2808680 | 0.82[ASN][1000 genomes] |
| rs2808692 | 0.86[ASN][1000 genomes] |
| rs7849815 | 0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv893610 | chr9:100324086-100496160 | Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 32 gene(s) | inside rSNPs | diseases |
| 2 | nsv1043753 | chr9:100458109-100599265 | Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 13 gene(s) | inside rSNPs | diseases |
| 3 | nsv614934 | chr9:100482976-100550253 | Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 7 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:3)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs953199 | ZNF484 | cis | cerebellum | SCAN |
| rs953199 | C9orf89 | cis | cerebellum | SCAN |
| rs953199 | C9orf156 | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr9:100482600-100483000 | ZNF genes & repeats | HSMMtube | muscle |
