Variant report
| Variant | rs6478743 |
|---|---|
| Chromosome Location | chr9:101289596-101289597 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:4)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:4 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr9:101281547..101284305-chr9:101287940..101290678,2 | K562 | blood: | |
| 2 | chr9:101288771..101290464-chr9:101295447..101297828,2 | MCF-7 | breast: | |
| 3 | chr9:101289571..101291142-chr9:101298750..101301335,2 | MCF-7 | breast: | |
| 4 | chr9:101287819..101290081-chr9:101317445..101319384,2 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000136928 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:17)
| rs_ID | r2[population] |
|---|---|
| rs10115107 | 0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs10121121 | 0.95[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs10121587 | 1.00[CEU][hapmap];1.00[EUR][1000 genomes] |
| rs10121704 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs10760389 | 0.94[ASW][hapmap];0.95[LWK][hapmap];0.93[MKK][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes] |
| rs10986579 | 0.96[AFR][1000 genomes] |
| rs10986744 | 1.00[CHD][hapmap] |
| rs12347388 | 0.95[EUR][1000 genomes] |
| rs4507885 | 1.00[CHD][hapmap] |
| rs55703227 | 1.00[EUR][1000 genomes] |
| rs55807407 | 1.00[EUR][1000 genomes] |
| rs55981436 | 0.83[EUR][1000 genomes] |
| rs56177517 | 0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs56339226 | 0.84[EUR][1000 genomes] |
| rs6478747 | 1.00[CEU][hapmap];0.84[TSI][hapmap];0.98[EUR][1000 genomes] |
| rs7855197 | 0.98[EUR][1000 genomes] |
| rs7857537 | 1.00[CHD][hapmap] |
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 | nsv430085 | chr9:100928245-101339645 | Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 19 gene(s) | inside rSNPs | diseases |
| 2 | nsv831665 | chr9:101170061-101367692 | Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 5 gene(s) | inside rSNPs | diseases |
| 3 | nsv614936 | chr9:101182698-101680380 | Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 21 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:3)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs6478743 | SLC35D2 | cis | parietal | SCAN |
| rs6478743 | TEX10 | cis | cerebellum | SCAN |
| rs6478743 | CTSL2 | cis | parietal | SCAN |
Chromatin state (count:0 , 50 per page) page:
| No data |
