Variant report
| Variant | rs17008180 |
|---|---|
| Chromosome Location | chr4:106406083-106406084 |
| allele | A/C |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:1)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:1 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr4:106393178..106395974-chr4:106403458..106406397,4 | K562 | blood: |
(count:1 , 50 per page) page:
1
| No. | lncRNA name | Chromosome Location | lncRNA alias |
|---|---|---|---|
| 1 | lnc-PPA2-1 | chr4:106405925-106406790 | NONHSAT097678 |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000138777 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:7)
| rs_ID | r2[population] |
|---|---|
| rs1048518 | 0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs12498981 | 0.89[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes] |
| rs12507480 | 0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap] |
| rs12644313 | 0.89[CEU][hapmap];0.81[EUR][1000 genomes] |
| rs2298733 | 0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs28723530 | 0.96[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs7660502 | 0.83[AFR][1000 genomes];0.96[EUR][1000 genomes];0.91[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 | nsv879699 | chr4:106212562-106698892 | Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 41 gene(s) | inside rSNPs | diseases |
| 2 | nsv830027 | chr4:106222010-106406738 | Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 27 gene(s) | inside rSNPs | diseases |
| 3 | nsv1002228 | chr4:106346206-106433381 | ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 19 gene(s) | inside rSNPs | diseases |
| 4 | nsv964078 | chr4:106404397-106407289 | ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:5)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs17008180 | PPA2 | Cis_1M | lymphoblastoid | RTeQTL |
| rs17008180 | UBE2D3 | cis | parietal | SCAN |
| rs17008180 | TET2 | cis | parietal | SCAN |
| rs17008180 | TET2 | cis | cerebellum | SCAN |
| rs17008180 | PPA2 | cis | multi-tissue | Pritchard |
Chromatin state (count:0 , 50 per page) page:
| No data |
