Variant report
| Variant | rs1280624 |
|---|---|
| Chromosome Location | chr3:136496690-136496691 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:3)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
| No data |
(count:3 , 50 per page) page:
1
| No. | lncRNA name | Chromosome Location | lncRNA alias |
|---|---|---|---|
| 1 | lnc-TMEM22-3 | chr3:136496640-136496711 | FPKM1_group_22046_transcript_2 |
| 2 | lnc-TMEM22-3 | chr3:136496678-136496968 | FPKM1_group_22046_transcript_2 |
| 3 | lnc-TMEM22-3 | chr3:136496640-136496711 | NONHSAT092285 |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:18)
| rs_ID | r2[population] |
|---|---|
| rs10513014 | 0.93[ASN][1000 genomes] |
| rs12107125 | 0.86[ASN][1000 genomes] |
| rs1280622 | 0.90[EUR][1000 genomes] |
| rs1681817 | 0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes] |
| rs1729951 | 0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs28489907 | 0.84[ASN][1000 genomes] |
| rs35874192 | 0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs4038578 | 0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes] |
| rs4408829 | 0.80[EUR][1000 genomes] |
| rs6439655 | 0.84[AMR][1000 genomes];0.87[EUR][1000 genomes] |
| rs6764567 | 0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes] |
| rs6789329 | 0.89[ASN][1000 genomes] |
| rs6802702 | 0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs7616204 | 0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes] |
| rs7637129 | 0.80[EUR][1000 genomes] |
| rs900818 | 0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes] |
| rs9825700 | 0.83[AMR][1000 genomes];0.89[EUR][1000 genomes] |
| rs9836231 | 0.81[AFR][1000 genomes];0.87[EUR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1006737 | chr3:136466188-136530743 | Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 29 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs1280624 | PCCB | Cis_1M | lymphoblastoid | RTeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr3:136496000-136497600 | Weak transcription | NH-A | brain |
