Variant report
| Variant | rs590198 |
|---|---|
| Chromosome Location | chr3:135953729-135953730 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:4)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:4 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr3:135929618..135932203-chr3:135951944..135954084,2 | K562 | blood: | |
| 2 | chr3:135914895..135917760-chr3:135953587..135955253,2 | MCF-7 | breast: | |
| 3 | chr3:135953105..135954994-chr3:135955237..135956991,2 | MCF-7 | breast: | |
| 4 | chr3:135914453..135916703-chr3:135953216..135954828,2 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000174579 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:16)
| rs_ID | r2[population] |
|---|---|
| rs1153870 | 1.00[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs1153872 | 0.98[AMR][1000 genomes];0.93[EUR][1000 genomes] |
| rs1153877 | 0.83[ASN][1000 genomes] |
| rs1279831 | 0.85[ASN][1000 genomes] |
| rs1279949 | 0.83[ASN][1000 genomes] |
| rs2459412 | 0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs3957816 | 0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs570621 | 0.83[ASN][1000 genomes] |
| rs589092 | 0.85[ASN][1000 genomes] |
| rs632251 | 0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs634559 | 0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs642075 | 0.83[ASN][1000 genomes] |
| rs661739 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs668437 | 0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs684195 | 0.83[ASN][1000 genomes] |
| rs895894 | 0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv869409 | chr3:135649101-136164174 | Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 50 gene(s) | inside rSNPs | diseases |
| 2 | nsv508246 | chr3:135922023-136038622 | Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 10 gene(s) | inside rSNPs | diseases |
| 3 | esv2760738 | chr3:135943988-135957333 | Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh | Chromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | n/a |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs590198 | PCCB | Cis_1M | lymphoblastoid | RTeQTL |
Chromatin state (count:0 , 50 per page) page:
| No data |
