Variant report
| Variant | rs6878612 |
|---|---|
| Chromosome Location | chr5:63262562-63262563 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:1)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:1 , 50 per page) page:
1
| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | POLR2A | chr5:63262498-63262631 | MCF10A-Er-Src | breast: | n/a | n/a |
| No data |
| No data |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| HTR1A | TF binding region |
rSNPs within LD-proxies of this variant (count:17)
| rs_ID | r2[population] |
|---|---|
| rs10042486 | 1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs10062933 | 0.94[EUR][1000 genomes] |
| rs1423691 | 0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs358524 | 0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes] |
| rs358526 | 0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs358527 | 0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes] |
| rs358528 | 0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs378864 | 0.86[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs421321 | 0.86[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs428731 | 0.86[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs6295 | 0.98[EUR][1000 genomes] |
| rs6449693 | 0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs7448318 | 0.99[ASN][1000 genomes] |
| rs749099 | 0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs7715837 | 0.96[CEU][hapmap];0.81[GIH][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap];0.96[EUR][1000 genomes] |
| rs878567 | 0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs970453 | 0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv598351 | chr5:63124140-63751144 | Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 7 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:3)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs6878612 | RGS7BP | cis | cerebellum | SCAN |
| rs6878612 | DCAF4L1 | trans | parietal | SCAN |
| rs6878612 | RNF180 | cis | cerebellum | SCAN |
Chromatin state (count:0 , 50 per page) page:
| No data |
