Variant report
| Variant | rs4671257 |
|---|---|
| Chromosome Location | chr2:55984530-55984531 |
| 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:30)
| rs_ID | r2[population] |
|---|---|
| rs10180127 | 0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs10207466 | 0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs10496050 | 0.88[JPT][hapmap] |
| rs1084522 | 0.88[JPT][hapmap] |
| rs1084525 | 0.88[JPT][hapmap] |
| rs11125598 | 0.90[AMR][1000 genomes] |
| rs1346792 | 0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs1346793 | 0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs1579497 | 0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs1975487 | 0.89[JPT][hapmap] |
| rs2586950 | 0.89[JPT][hapmap] |
| rs2627765 | 0.88[JPT][hapmap] |
| rs2627775 | 0.88[JPT][hapmap] |
| rs2627776 | 0.90[JPT][hapmap] |
| rs35504023 | 0.88[JPT][hapmap] |
| rs4672066 | 0.85[ASN][1000 genomes] |
| rs6545506 | 0.86[JPT][hapmap] |
| rs6717410 | 0.89[AMR][1000 genomes];0.87[ASN][1000 genomes] |
| rs6728604 | 0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs706548 | 0.88[JPT][hapmap] |
| rs7557041 | 0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs7594133 | 0.83[AMR][1000 genomes] |
| rs782584 | 0.88[JPT][hapmap] |
| rs782586 | 0.88[JPT][hapmap] |
| rs782588 | 0.88[JPT][hapmap] |
| rs782590 | 0.86[JPT][hapmap] |
| rs782595 | 0.90[JPT][hapmap] |
| rs782602 | 0.88[JPT][hapmap] |
| rs782606 | 1.00[JPT][hapmap] |
| rs782652 | 0.88[JPT][hapmap] |
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 | nsv531374 | chr2:55653723-56299784 | Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 56 gene(s) | inside rSNPs | diseases |
| 2 | nsv1008452 | chr2:55809191-55987274 | Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 27 gene(s) | inside rSNPs | diseases |
| 3 | nsv999962 | chr2:55976574-56011517 | Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS | Chromatin interactive region | 1 gene(s) | inside rSNPs | diseases |
| 4 | nsv997683 | chr2:55976574-56013875 | Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Strong transcription | Chromatin interactive region | 1 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs4671257 | PNPT1 | Cis_1M | lymphoblastoid | RTeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr2:55972200-55986600 | Weak transcription | Breast variant Human Mammary Epithelial Cells (vHMEC) | Breast |
