Variant report
| Variant | rs11630087 |
|---|---|
| Chromosome Location | chr15:75261673-75261674 |
| allele | G/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:23)
| rs_ID | r2[population] |
|---|---|
| rs11072514 | 0.82[AMR][1000 genomes] |
| rs1133323 | 0.80[AMR][1000 genomes] |
| rs11630592 | 0.84[AMR][1000 genomes] |
| rs11636892 | 0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs11639413 | 0.87[AMR][1000 genomes] |
| rs11856413 | 0.80[AMR][1000 genomes] |
| rs12901190 | 0.84[AMR][1000 genomes] |
| rs12903370 | 0.82[AMR][1000 genomes] |
| rs12904326 | 0.80[AMR][1000 genomes] |
| rs12909335 | 0.80[AMR][1000 genomes] |
| rs12912343 | 0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs12912839 | 0.80[AMR][1000 genomes] |
| rs2044157 | 0.84[AMR][1000 genomes] |
| rs2415251 | 0.87[AMR][1000 genomes] |
| rs34063670 | 0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes] |
| rs34307821 | 0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs34799293 | 0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes] |
| rs35556055 | 0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs35882241 | 0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs4886413 | 0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs56338926 | 0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs62029217 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs7495664 | 0.80[AMR][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 | nsv569993 | chr15:75242155-75483752 | Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 72 gene(s) | inside rSNPs | diseases |
| 2 | nsv1612 | chr15:75247725-75281284 | Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 46 gene(s) | inside rSNPs | diseases |
| 3 | nsv977735 | chr15:75257534-75268830 | Enhancers Bivalent Enhancer Weak transcription | Chromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:5)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs11630087 | SCAMP2 | Cis_1M | lymphoblastoid | RTeQTL |
| rs11630087 | SCAMP5 | cis | lung | GTEx |
| rs11630087 | SCAMP2 | cis | Whole Blood | GTEx |
| rs11630087 | COX5A | Cis_1M | lymphoblastoid | RTeQTL |
| rs11630087 | SCAMP5 | cis | Artery Tibial | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr15:75257600-75270800 | Weak transcription | H1 Derived Mesenchymal Stem Cells | ES cell derived |
