Variant report
| Variant | rs4652417 |
|---|---|
| Chromosome Location | chr1:179559456-179559457 |
| 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:26)
| rs_ID | r2[population] |
|---|---|
| rs1060775 | 1.00[CHD][hapmap] |
| rs10733002 | 0.81[AMR][1000 genomes] |
| rs1079292 | 0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes] |
| rs10913807 | 1.00[CHD][hapmap] |
| rs1328595 | 1.00[GIH][hapmap];1.00[TSI][hapmap] |
| rs1410590 | 1.00[CHD][hapmap] |
| rs1831180 | 1.00[CHD][hapmap] |
| rs1887815 | 0.83[YRI][hapmap] |
| rs1928004 | 1.00[CHD][hapmap] |
| rs1999069 | 1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs2026014 | 0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes] |
| rs3930537 | 0.94[YRI][hapmap] |
| rs4391629 | 0.81[AMR][1000 genomes] |
| rs4422967 | 0.81[AMR][1000 genomes] |
| rs4651044 | 1.00[GIH][hapmap];1.00[TSI][hapmap] |
| rs4652421 | 1.00[GIH][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs4652423 | 0.81[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs6696896 | 1.00[CHD][hapmap] |
| rs749960 | 1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes] |
| rs7512551 | 1.00[CHD][hapmap] |
| rs7514875 | 0.81[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs7517766 | 0.87[ASW][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap] |
| rs7518557 | 0.88[YRI][hapmap] |
| rs7549258 | 1.00[CHB][hapmap] |
| rs928016 | 1.00[CHD][hapmap] |
| rs964982 | 1.00[CHD][hapmap] |
Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv946524 | chr1:179558860-179559970 | Weak transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs4652417 | SAMSN1 | trans | lymphoblastoid | seeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:179556000-179560600 | Weak transcription | Right Atrium | heart |
| 2 | chr1:179558200-179560600 | Weak transcription | iPS DF 19.11 Cell Line | embryonic stem cell |
