Variant report
| Variant | rs565418 |
|---|---|
| Chromosome Location | chr1:166649076-166649077 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:1 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr1:166646941..166649899-chr1:166808639..166811427,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000143157 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:23)
| rs_ID | r2[population] |
|---|---|
| rs10737530 | 1.00[CHD][hapmap] |
| rs1561844 | 1.00[CHD][hapmap] |
| rs34900988 | 0.97[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs489060 | 1.00[YRI][hapmap] |
| rs489144 | 1.00[CHD][hapmap] |
| rs494467 | 1.00[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs502594 | 0.92[AMR][1000 genomes];0.88[EUR][1000 genomes] |
| rs503909 | 1.00[CHD][hapmap] |
| rs503961 | 0.97[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs506349 | 0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs511860 | 1.00[CHD][hapmap] |
| rs517224 | 1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs523900 | 0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs526625 | 1.00[YRI][hapmap] |
| rs540253 | 1.00[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs543249 | 0.97[AMR][1000 genomes];0.96[EUR][1000 genomes] |
| rs554914 | 1.00[CHD][hapmap] |
| rs562914 | 0.97[AMR][1000 genomes];0.95[EUR][1000 genomes] |
| rs565064 | 1.00[CHD][hapmap] |
| rs569407 | 0.95[AFR][1000 genomes] |
| rs579671 | 1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[YRI][hapmap] |
| rs858818 | 0.81[CEU][hapmap] |
| rs9726160 | 0.87[EUR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv916491 | chr1:166000783-166948513 | Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 38 gene(s) | inside rSNPs | diseases |
| 2 | esv2757759 | chr1:166491879-166650985 | Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
| 3 | esv2758975 | chr1:166491879-166650985 | ZNF genes & repeats Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
| 4 | esv2752389 | chr1:166625342-166706342 | Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS | TF binding regionChromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
| 5 | nsv947550 | chr1:166647096-166673303 | Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer | Chromatin interactive regionlncRNA | 1 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:4)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs565418 | FCGR2A | cis | parietal | SCAN |
| rs565418 | PPOX | cis | parietal | SCAN |
| rs565418 | RGS4 | cis | parietal | SCAN |
| rs565418 | ALDH9A1 | cis | parietal | SCAN |
Chromatin state (count:0 , 50 per page) page:
| No data |
