Variant report
| Variant | rs9871303 |
|---|---|
| Chromosome Location | chr3:144221910-144221911 |
| 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 | chr1:153580940..153582973-chr3:144219455..144221982,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000188643 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:21)
| rs_ID | r2[population] |
|---|---|
| rs1178898 | 0.91[AMR][1000 genomes];0.95[EUR][1000 genomes] |
| rs1178902 | 0.91[AMR][1000 genomes];0.95[EUR][1000 genomes] |
| rs13076501 | 0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs1527231 | 0.93[AMR][1000 genomes];0.96[EUR][1000 genomes] |
| rs1656986 | 0.96[AMR][1000 genomes];0.96[EUR][1000 genomes] |
| rs1726523 | 1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes] |
| rs1726525 | 0.95[AMR][1000 genomes];0.95[EUR][1000 genomes] |
| rs1726537 | 0.98[AMR][1000 genomes];0.96[EUR][1000 genomes] |
| rs1880902 | 0.91[AMR][1000 genomes];0.90[EUR][1000 genomes] |
| rs2575182 | 0.87[AMR][1000 genomes];0.90[EUR][1000 genomes] |
| rs2575187 | 0.83[AMR][1000 genomes];0.84[EUR][1000 genomes] |
| rs2694958 | 0.82[AMR][1000 genomes];0.84[EUR][1000 genomes] |
| rs2717378 | 0.91[AMR][1000 genomes];0.90[EUR][1000 genomes] |
| rs4511940 | 1.00[ASN][1000 genomes] |
| rs4681332 | 0.93[EUR][1000 genomes] |
| rs759968 | 0.91[AMR][1000 genomes];0.95[EUR][1000 genomes] |
| rs7628404 | 0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs9845422 | 0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs9852425 | 1.00[ASN][1000 genomes] |
| rs9857731 | 1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs9864125 | 0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv532633 | chr3:143802417-144440646 | Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 8 gene(s) | inside rSNPs | diseases |
| 2 | nsv591928 | chr3:144050897-144822081 | Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats | Chromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
| 3 | esv2756108 | chr3:144177836-144301659 | Enhancers Flanking Active TSS Weak transcription Active TSS | Chromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
| 4 | nsv877571 | chr3:144188561-144291254 | Enhancers Weak transcription Flanking Active TSS | Chromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs9871303 | CHAF1A | trans | lymphoblastoid | RTeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr3:144220400-144222000 | Enhancers | hESC Derived CD56+ Ectoderm Cultured Cells | ES cell derived |
| 2 | chr3:144220600-144222200 | Weak transcription | H1 Derived Neuronal Progenitor Cultured Cells | ES cell derived |
