Variant report
| Variant | rs1479521 |
|---|---|
| Chromosome Location | chr15:92734540-92734541 |
| allele | C/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:14)
| rs_ID | r2[population] |
|---|---|
| rs11074058 | 0.86[CHB][hapmap] |
| rs3956218 | 0.97[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs4304975 | 0.89[ASN][1000 genomes] |
| rs4304976 | 0.89[ASN][1000 genomes] |
| rs4777930 | 0.82[GIH][hapmap] |
| rs4778040 | 0.96[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs59933941 | 0.81[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs60775541 | 0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs62009277 | 0.84[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs62011490 | 0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs62011492 | 1.00[ASN][1000 genomes] |
| rs720680 | 0.85[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs8028773 | 0.96[EUR][1000 genomes] |
| rs9920312 | 1.00[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv948621 | chr15:92688981-93158095 | Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 28 gene(s) | inside rSNPs | diseases |
| 2 | nsv1037878 | chr15:92713130-92739827 | Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 3 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:3)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs1479521 | RGMA | cis | parietal | SCAN |
| rs1479521 | NCRNA00052 | cis | parietal | SCAN |
| rs1479521 | MESP1 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr15:92733600-92741000 | Weak transcription | iPS DF 19.11 Cell Line | embryonic stem cell |
