Variant report
| Variant | rs6420121 |
|---|---|
| Chromosome Location | chr5:164398549-164398550 |
| allele | A/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:7)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:7 , 50 per page) page:
1
| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | GATA3 | chr5:164398530-164399008 | T-47D | breast: | n/a | n/a |
| 2 | GATA3 | chr5:164398501-164398962 | T-47D | breast: | n/a | n/a |
| 3 | ESR1 | chr5:164398513-164398978 | T-47D | breast: | n/a | n/a |
| 4 | JUND | chr5:164398516-164399379 | T-47D | breast: | n/a | n/a |
| 5 | JUND | chr5:164398485-164399063 | T-47D | breast: | n/a | n/a |
| 6 | EP300 | chr5:164398485-164399019 | T-47D | breast: | n/a | n/a |
| 7 | FOXA1 | chr5:164398521-164399015 | T-47D | breast: | n/a | n/a |
| No data |
| No data |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000241956 | TF binding region |
rSNPs within LD-proxies of this variant (count:12)
| rs_ID | r2[population] |
|---|---|
| rs10066727 | 0.89[EUR][1000 genomes] |
| rs13173293 | 0.89[ASN][1000 genomes] |
| rs35406848 | 0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs35411130 | 0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs36057000 | 0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs4131412 | 0.92[ASN][1000 genomes] |
| rs4530780 | 0.85[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs4582301 | 0.87[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs6859274 | 0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs7448333 | 0.89[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs7448803 | 0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs9790906 | 0.92[EUR][1000 genomes];0.90[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 | nsv995060 | chr5:163660200-164620500 | Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 11 gene(s) | inside rSNPs | diseases |
| 2 | nsv528624 | chr5:164319435-164701201 | Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
| 3 | nsv600242 | chr5:164391457-164466785 | Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS | TF binding regionChromatin interactive regionlncRNA | 1 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs6420121 | NUDCD2 | cis | cerebellum | SCAN |
| rs6420121 | WWC1 | cis | cerebellum | SCAN |
Chromatin state (count:0 , 50 per page) page:
| No data |
