Variant report
| Variant | rs3779790 |
|---|---|
| Chromosome Location | chr8:87677043-87677044 |
| 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 | FOS | chr8:87676948-87677214 | MCF10A-Er-Src | breast: | n/a | n/a |
| No data |
| No data |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| GOLGA2P1 | TF binding region |
| UBE2Q2P10 | TF binding region |
rSNPs within LD-proxies of this variant (count:16)
| rs_ID | r2[population] |
|---|---|
| rs10094222 | 0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap] |
| rs1009574 | 0.92[CEU][hapmap];0.91[JPT][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes] |
| rs10216710 | 0.89[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap] |
| rs10216953 | 0.85[CEU][hapmap];0.95[JPT][hapmap] |
| rs13258590 | 0.80[CHB][hapmap];0.86[JPT][hapmap] |
| rs13268738 | 0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes] |
| rs13278423 | 0.82[JPT][hapmap] |
| rs1441243 | 0.88[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap] |
| rs16916427 | 0.85[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap] |
| rs16916907 | 0.81[JPT][hapmap] |
| rs3735967 | 0.94[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap] |
| rs3779801 | 0.81[CEU][hapmap] |
| rs59109039 | 0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes] |
| rs7842410 | 0.86[CHD][hapmap] |
| rs9297941 | 0.81[CEU][hapmap];0.80[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap] |
| rs978134 | 0.82[JPT][hapmap] |
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 | nsv1023510 | chr8:87429001-87874948 | Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 31 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs3779790 | RIPK2 | cis | parietal | SCAN |
| rs3779790 | RBM24 | trans | parietal | SCAN |
Chromatin state (count:0 , 50 per page) page:
| No data |
