Variant report
| Variant | rs4548435 |
|---|---|
| Chromosome Location | chr1:159334850-159334851 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:1)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:1 , 50 per page) page:
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| No data |
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| No data |
| Variant related genes | Relation type |
|---|---|
| OR10J8P | TF binding region |
rSNPs within LD-proxies of this variant (count:11)
| rs_ID | r2[population] |
|---|---|
| rs11265175 | 0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs12409540 | 1.00[YRI][hapmap] |
| rs17422585 | 0.82[ASW][hapmap] |
| rs2427829 | 0.84[AFR][1000 genomes];0.87[ASN][1000 genomes] |
| rs2427830 | 0.87[ASN][1000 genomes] |
| rs3845625 | 1.00[YRI][hapmap] |
| rs6678381 | 0.87[GIH][hapmap] |
| rs7511872 | 1.00[YRI][hapmap] |
| rs7522607 | 0.82[ASW][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap] |
| rs7549785 | 0.83[MKK][hapmap];1.00[YRI][hapmap] |
| rs7553515 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page:
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| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv872487 | chr1:159196765-159342439 | Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 6 gene(s) | inside rSNPs | diseases |
| 2 | nsv872488 | chr1:159218266-159336948 | Flanking Active TSS Enhancers Weak transcription Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 6 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:6)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs4548435 | EFNA3 | cis | cerebellum | SCAN |
| rs4548435 | CD1D | cis | cerebellum | SCAN |
| rs4548435 | FCGR3A | cis | parietal | SCAN |
| rs4548435 | PMF1 | cis | parietal | SCAN |
| rs4548435 | OR10K1 | cis | parietal | SCAN |
| rs4548435 | CD5L | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:159332800-159336200 | Weak transcription | Pancreas | Pancrea |
