Variant report
| Variant | rs6663218 |
|---|---|
| Chromosome Location | chr1:94404238-94404239 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:8)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:8 , 50 per page) page:
1
| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | REST | chr1:94403983-94404505 | MCF-7 | breast: | n/a | chr1:94404220-94404229 |
| 2 | TEAD4 | chr1:94403957-94404448 | A549 | lung: | n/a | n/a |
| 3 | REST | chr1:94404088-94404324 | Hela-S3 | cervix: | n/a | chr1:94404220-94404229 |
| 4 | REST | chr1:94404146-94404263 | K562 | blood: | n/a | chr1:94404220-94404229 |
| 5 | REST | chr1:94403952-94404475 | ECC-1 | luminal epithelium: | n/a | chr1:94404220-94404229 |
| 6 | REST | chr1:94403959-94404415 | MCF-7 | breast: | n/a | chr1:94404220-94404229 |
| 7 | REST | chr1:94404071-94404390 | ECC-1 | luminal epithelium: | n/a | chr1:94404220-94404229 |
| 8 | REST | chr1:94404104-94404407 | PFSK-1 | brain: | n/a | chr1:94404220-94404229 |
| No data |
| No data |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000233129 | TF binding region |
rSNPs within LD-proxies of this variant (count:19)
| rs_ID | r2[population] |
|---|---|
| rs10489602 | 0.82[JPT][hapmap] |
| rs10874810 | 0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs11165022 | 0.84[CHB][hapmap];0.91[JPT][hapmap] |
| rs11165026 | 0.84[CHB][hapmap];0.91[JPT][hapmap] |
| rs11165036 | 0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs12041975 | 0.84[CHB][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap] |
| rs12140446 | 0.90[CHB][hapmap];0.82[JPT][hapmap] |
| rs12563495 | 0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs2143992 | 0.84[CHB][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap] |
| rs2273166 | 0.84[CHB][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap] |
| rs2391315 | 0.82[GIH][hapmap];0.95[JPT][hapmap] |
| rs2747045 | 0.82[JPT][hapmap] |
| rs4075523 | 0.82[JPT][hapmap] |
| rs4240956 | 0.82[JPT][hapmap] |
| rs4847264 | 0.84[CHB][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap] |
| rs6681265 | 0.84[CHB][hapmap];0.91[JPT][hapmap] |
| rs743111 | 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[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs7520019 | 0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs7521934 | 0.85[AFR][1000 genomes];0.84[AMR][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 | nsv516137 | chr1:94404238-94504545 | Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs6663218 | RP11-488P3.1 | cis | Muscle Skeletal | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:94375600-94421200 | Weak transcription | Breast variant Human Mammary Epithelial Cells (vHMEC) | Breast |
