Variant report
| Variant | rs6987076 |
|---|---|
| Chromosome Location | chr8:52878790-52878791 |
| allele | A/G |
| 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:25)
| rs_ID | r2[population] |
|---|---|
| rs12550430 | 0.82[ASN][1000 genomes] |
| rs1996260 | 0.90[JPT][hapmap];0.82[ASN][1000 genomes] |
| rs2090259 | 0.82[ASN][1000 genomes] |
| rs2090260 | 0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs2102727 | 0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs4147306 | 1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs4873622 | 0.85[JPT][hapmap];0.82[ASN][1000 genomes] |
| rs4873624 | 0.81[ASN][1000 genomes] |
| rs4873625 | 0.81[ASN][1000 genomes] |
| rs4873626 | 0.82[ASN][1000 genomes] |
| rs4873627 | 0.82[ASN][1000 genomes] |
| rs4873628 | 0.82[ASN][1000 genomes] |
| rs4873629 | 0.82[ASN][1000 genomes] |
| rs4873630 | 0.82[ASN][1000 genomes] |
| rs4873631 | 0.82[ASN][1000 genomes] |
| rs4873632 | 0.85[JPT][hapmap];0.82[ASN][1000 genomes] |
| rs55996614 | 0.82[ASN][1000 genomes] |
| rs57711556 | 0.82[ASN][1000 genomes] |
| rs6473670 | 0.90[JPT][hapmap];0.82[ASN][1000 genomes] |
| rs6473671 | 0.85[JPT][hapmap];0.82[ASN][1000 genomes] |
| rs6473672 | 0.85[JPT][hapmap];0.82[ASN][1000 genomes] |
| rs6982231 | 0.85[JPT][hapmap];0.82[ASN][1000 genomes] |
| rs6993367 | 0.86[CHB][hapmap];1.00[YRI][hapmap] |
| rs7004360 | 0.82[ASN][1000 genomes] |
| rs7820670 | 0.94[EUR][1000 genomes];0.86[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv817615 | chr8:52252405-53023384 | Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 22 gene(s) | inside rSNPs | diseases |
| 2 | nsv1018429 | chr8:52411443-52878946 | Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 19 gene(s) | inside rSNPs | diseases |
| 3 | nsv1034856 | chr8:52411443-52886765 | Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 19 gene(s) | inside rSNPs | diseases |
| 4 | nsv1031672 | chr8:52872448-52917469 | Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs6987076 | PCMTD1 | Cis_1M | lymphoblastoid | RTeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr8:52875400-52884800 | Weak transcription | Pancreas | Pancrea |
| 2 | chr8:52875800-52886200 | Weak transcription | Breast variant Human Mammary Epithelial Cells (vHMEC) | Breast |
