Variant report
| Variant | rs10209546 |
|---|---|
| Chromosome Location | chr2:53408321-53408322 |
| allele | G/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- 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 | chr2:53405292..53406981-chr2:53407516..53409368,2 | K562 | blood: |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:18)
| rs_ID | r2[population] |
|---|---|
| rs10196500 | 0.94[AFR][1000 genomes] |
| rs10496017 | 0.96[AFR][1000 genomes] |
| rs10496018 | 0.90[AFR][1000 genomes] |
| rs12612804 | 0.80[ASN][1000 genomes] |
| rs1424976 | 0.96[AFR][1000 genomes] |
| rs2113821 | 0.88[AFR][1000 genomes] |
| rs2113822 | 0.84[AFR][1000 genomes] |
| rs41377747 | 0.86[ASN][1000 genomes] |
| rs4672236 | 0.86[ASN][1000 genomes] |
| rs4672241 | 0.99[AFR][1000 genomes] |
| rs4672242 | 0.93[AFR][1000 genomes] |
| rs4672243 | 0.96[AFR][1000 genomes] |
| rs4672244 | 0.85[AFR][1000 genomes] |
| rs59874342 | 0.86[ASN][1000 genomes] |
| rs60442673 | 0.86[ASN][1000 genomes] |
| rs6736253 | 0.99[AFR][1000 genomes] |
| rs6739172 | 0.91[AFR][1000 genomes];0.83[AMR][1000 genomes] |
| rs72908171 | 0.86[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv520722 | chr2:53039770-53421015 | Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
| 2 | esv2751897 | chr2:53358205-53475338 | Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS | Chromatin interactive region | 3 gene(s) | inside rSNPs | diseases |
| 3 | nsv1011032 | chr2:53384170-53433055 | Weak transcription Enhancers Bivalent Enhancer | Chromatin interactive region | n/a | inside rSNPs | diseases |
| 4 | nsv1002145 | chr2:53387912-53832213 | Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 6 gene(s) | inside rSNPs | diseases |
| 5 | nsv535718 | chr2:53387912-53832213 | Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 6 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:10)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs10209546 | LRTM1 | trans | brain | seeQTL |
| rs10209546 | SLC5A7 | trans | brain | seeQTL |
| rs10209546 | TTR | trans | brain | seeQTL |
| rs10209546 | PDE6H | trans | brain | seeQTL |
| rs10209546 | GUCA1C | trans | brain | seeQTL |
| rs10209546 | DEFB119 | trans | brain | seeQTL |
| rs10209546 | C2CD4B | trans | brain | seeQTL |
| rs10209546 | SH2D2A | trans | brain | seeQTL |
| rs10209546 | CRX | trans | brain | seeQTL |
| rs10209546 | ASMT | trans | brain | seeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr2:53402200-53409000 | Weak transcription | Fetal Lung | lung |
