Variant report
| Variant | rs6446159 |
|---|---|
| Chromosome Location | chr3:60877992-60877993 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
| No data |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:20)
| rs_ID | r2[population] |
|---|---|
| rs11130798 | 0.82[CEU][hapmap] |
| rs11926529 | 0.82[CEU][hapmap];0.89[MEX][hapmap] |
| rs13097786 | 0.90[CEU][hapmap];0.88[EUR][1000 genomes] |
| rs1447917 | 0.85[CHB][hapmap];1.00[JPT][hapmap] |
| rs1562521 | 0.85[CHB][hapmap];1.00[JPT][hapmap] |
| rs35353184 | 0.96[EUR][1000 genomes] |
| rs35673396 | 0.88[EUR][1000 genomes] |
| rs6763967 | 0.81[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs6764919 | 0.82[AMR][1000 genomes];0.99[EUR][1000 genomes] |
| rs6765028 | 0.95[CEU][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes] |
| rs6785095 | 0.82[TSI][hapmap] |
| rs6785481 | 0.95[EUR][1000 genomes] |
| rs6804218 | 0.97[EUR][1000 genomes] |
| rs7630291 | 0.86[CEU][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes] |
| rs7634868 | 0.82[CEU][hapmap];0.89[MEX][hapmap] |
| rs7640419 | 0.83[CEU][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes] |
| rs9808931 | 0.82[CEU][hapmap];0.89[MEX][hapmap] |
| rs9819641 | 0.85[CHB][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes] |
| rs9826649 | 0.95[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes] |
| rs9827069 | 0.88[EUR][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 | nsv534038 | chr3:60781917-60993082 | Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 1 gene(s) | inside rSNPs | diseases |
| 2 | esv2757872 | chr3:60781943-61019003 | ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 1 gene(s) | inside rSNPs | diseases |
| 3 | esv2759152 | chr3:60781943-61220809 | Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 1 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs6446159 | TDGF1 | trans | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr3:60872600-60879600 | Weak transcription | HUES64 Cell Line | embryonic stem cell |
