Variant report
| Variant | rs1268459 |
|---|---|
| Chromosome Location | chr10:116923274-116923275 |
| allele | A/C |
| 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:31)
| rs_ID | r2[population] |
|---|---|
| rs1010610 | 0.87[EUR][1000 genomes] |
| rs10787557 | 0.80[EUR][1000 genomes] |
| rs10885658 | 0.82[EUR][1000 genomes];0.81[ASN][1000 genomes] |
| rs10885659 | 0.80[ASN][1000 genomes] |
| rs10885660 | 0.80[ASN][1000 genomes] |
| rs10885661 | 0.80[EUR][1000 genomes] |
| rs11197084 | 0.82[EUR][1000 genomes] |
| rs11197093 | 0.88[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs11197094 | 0.80[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs12360503 | 0.82[EUR][1000 genomes] |
| rs1264748 | 0.85[EUR][1000 genomes] |
| rs1264756 | 0.81[AMR][1000 genomes];0.89[EUR][1000 genomes] |
| rs1264763 | 0.82[AMR][1000 genomes];0.90[EUR][1000 genomes] |
| rs1264765 | 0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes] |
| rs1264768 | 0.87[EUR][1000 genomes] |
| rs1264782 | 0.87[EUR][1000 genomes] |
| rs1264783 | 0.84[EUR][1000 genomes] |
| rs1264794 | 0.81[EUR][1000 genomes];0.83[ASN][1000 genomes] |
| rs1264795 | 0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes] |
| rs1264796 | 0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes] |
| rs1264799 | 0.87[EUR][1000 genomes] |
| rs1268460 | 0.87[EUR][1000 genomes] |
| rs1268916 | 0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs1269602 | 0.81[ASN][1000 genomes] |
| rs1270442 | 0.85[EUR][1000 genomes] |
| rs1270654 | 0.87[EUR][1000 genomes] |
| rs1663157 | 0.83[EUR][1000 genomes] |
| rs1899718 | 0.82[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs2265930 | 0.84[EUR][1000 genomes] |
| rs2492980 | 0.81[EUR][1000 genomes] |
| rs2492981 | 0.85[EUR][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 | esv3435429 | chr10:116394152-117006347 | Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 21 gene(s) | inside rSNPs | diseases |
| 2 | nsv831998 | chr10:116847998-116969618 | Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription | TF binding regionCpG islandChromatin interactive region | 2 gene(s) | inside rSNPs | diseases |
| 3 | nsv869279 | chr10:116884639-117032437 | Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription | TF binding regionChromatin interactive region | 1 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs1268459 | ATRNL1 | cis | Esophagus Muscularis | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr10:116912000-116925600 | Weak transcription | H9 Derived Neuron Cultured Cells | ES cell derived |
| 2 | chr10:116919800-116925800 | Weak transcription | H9 Derived Neuronal Progenitor Cultured Cells | ES cell derived |
