Variant report
| Variant | rs3748653 |
|---|---|
| Chromosome Location | chr1:102359002-102359003 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:2)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
| No data |
(count:2 , 50 per page) page:
1
| No. | lncRNA name | Chromosome Location | lncRNA alias |
|---|---|---|---|
| 1 | lnc-S1PR1-13 | chr1:102358613-102360299 | NONHSAT004867 |
| 2 | lnc-S1PR1-13 | chr1:102358661-102359603 | NONHSAT004869 |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:19)
| rs_ID | r2[population] |
|---|---|
| rs1008809 | 0.81[CHD][hapmap];0.91[JPT][hapmap] |
| rs10493968 | 0.91[JPT][hapmap] |
| rs10493969 | 0.91[JPT][hapmap] |
| rs11164323 | 0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs11809591 | 0.97[ASN][1000 genomes] |
| rs12748614 | 0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs1999795 | 0.81[ASN][1000 genomes] |
| rs2000149 | 0.81[CHD][hapmap];0.91[JPT][hapmap] |
| rs2000150 | 0.81[CHD][hapmap];0.90[JPT][hapmap] |
| rs2211297 | 1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.90[YRI][hapmap] |
| rs2879348 | 0.90[JPT][hapmap] |
| rs4908198 | 0.81[CHD][hapmap];0.95[JPT][hapmap] |
| rs4908200 | 0.95[JPT][hapmap] |
| rs6577281 | 0.84[ASN][1000 genomes] |
| rs6662872 | 0.91[JPT][hapmap] |
| rs728323 | 0.82[ASN][1000 genomes] |
| rs7524443 | 0.90[JPT][hapmap] |
| rs7526689 | 0.95[JPT][hapmap] |
| rs7531673 | 0.81[CHD][hapmap];0.91[JPT][hapmap] |
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 | nsv522921 | chr1:102170295-102876392 | Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 17 gene(s) | inside rSNPs | diseases |
| 2 | nsv522156 | chr1:102309649-102421714 | Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs3748653 | OLFM3 | cis | cerebellum | SCAN |
| rs3748653 | AMY2B | cis | cerebellum | SCAN |
Chromatin state (count:0 , 50 per page) page:
| No data |
