Variant report
| Variant | rs7817558 |
|---|---|
| Chromosome Location | chr8:52881962-52881963 |
| allele | A/T |
| 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:35)
| rs_ID | r2[population] |
|---|---|
| rs10087958 | 0.82[ASN][1000 genomes] |
| rs10453128 | 0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs12541514 | 0.80[ASN][1000 genomes] |
| rs12541693 | 0.82[ASN][1000 genomes] |
| rs12544671 | 0.80[ASN][1000 genomes] |
| rs12544872 | 0.82[ASN][1000 genomes] |
| rs12545423 | 0.82[ASN][1000 genomes] |
| rs12545755 | 0.81[ASN][1000 genomes] |
| rs12546159 | 0.81[ASN][1000 genomes] |
| rs12547887 | 0.81[ASN][1000 genomes] |
| rs12678795 | 0.80[ASN][1000 genomes] |
| rs16916966 | 0.81[ASN][1000 genomes] |
| rs16916968 | 0.82[ASN][1000 genomes] |
| rs16917017 | 0.81[ASN][1000 genomes] |
| rs16917024 | 0.80[ASN][1000 genomes] |
| rs16917026 | 0.80[ASN][1000 genomes] |
| rs16917029 | 0.80[ASN][1000 genomes] |
| rs16917030 | 0.80[ASN][1000 genomes] |
| rs16917031 | 0.80[ASN][1000 genomes] |
| rs2138297 | 0.82[ASN][1000 genomes] |
| rs2176119 | 0.82[ASN][1000 genomes] |
| rs55870400 | 0.80[ASN][1000 genomes] |
| rs73681421 | 0.82[ASN][1000 genomes] |
| rs73681429 | 0.80[ASN][1000 genomes] |
| rs73681430 | 0.80[ASN][1000 genomes] |
| rs73681431 | 0.80[ASN][1000 genomes] |
| rs7813414 | 0.84[ASN][1000 genomes] |
| rs7816834 | 1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs7817892 | 1.00[ASN][1000 genomes] |
| rs7819892 | 0.82[ASN][1000 genomes] |
| rs7833668 | 0.82[ASN][1000 genomes] |
| rs7834181 | 0.86[ASN][1000 genomes] |
| rs7838307 | 0.94[ASN][1000 genomes] |
| rs7844884 | 0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs877248 | 0.82[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 | 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 |
| 3 | 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 |
| 4 | nsv1020673 | chr8:52878946-52917469 | Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer | Chromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs7817558 | 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 |
| 3 | chr8:52881600-52886200 | Weak transcription | Psoas Muscle | Psoas |
