Variant report
| Variant | rs12192520 |
|---|---|
| Chromosome Location | chr6:54279637-54279638 |
| 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:26)
| rs_ID | r2[population] |
|---|---|
| rs10456174 | 0.93[TSI][hapmap] |
| rs10456681 | 0.92[TSI][hapmap] |
| rs10456682 | 0.80[AMR][1000 genomes] |
| rs10456683 | 0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs10456684 | 1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs10498797 | 1.00[CHD][hapmap];0.93[TSI][hapmap] |
| rs10948812 | 0.83[CEU][hapmap] |
| rs10948813 | 0.92[TSI][hapmap] |
| rs10948814 | 0.93[TSI][hapmap] |
| rs10948817 | 0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs12189890 | 0.80[AMR][1000 genomes] |
| rs12193891 | 0.93[TSI][hapmap] |
| rs12204930 | 0.80[AMR][1000 genomes] |
| rs12210322 | 0.80[AMR][1000 genomes] |
| rs12213596 | 0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs12661397 | 0.93[TSI][hapmap] |
| rs12663327 | 1.00[CHD][hapmap];0.93[TSI][hapmap] |
| rs12664425 | 0.80[AMR][1000 genomes] |
| rs1508632 | 0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs2063238 | 0.80[AMR][1000 genomes] |
| rs59459598 | 0.80[AMR][1000 genomes] |
| rs59508393 | 0.80[AMR][1000 genomes] |
| rs7750024 | 0.80[AMR][1000 genomes] |
| rs9283920 | 0.80[CEU][hapmap] |
| rs9382326 | 0.93[TSI][hapmap] |
| rs9395943 | 0.93[TSI][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 | nsv1067663 | chr6:53796341-54449718 | Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 14 gene(s) | inside rSNPs | diseases |
| 2 | nsv529158 | chr6:53796341-54449718 | Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 14 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs12192520 | GCLC | cis | parietal | SCAN |
| rs12192520 | PAQR8 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr6:54269400-54284400 | Weak transcription | Breast variant Human Mammary Epithelial Cells (vHMEC) | Breast |
