Variant report
| Variant | rs12660499 |
|---|---|
| Chromosome Location | chr6:30194873-30194874 |
| 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 | chr6:30194307..30196564-chr6:30200875..30202443,2 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000270604 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:22)
| rs_ID | r2[population] |
|---|---|
| rs12175655 | 0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes] |
| rs17188113 | 0.82[EUR][1000 genomes] |
| rs2074477 | 0.83[EUR][1000 genomes] |
| rs2187980 | 0.84[EUR][1000 genomes];0.84[ASN][1000 genomes] |
| rs2239531 | 0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs2284167 | 0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs2284171 | 0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs2517602 | 0.88[ASN][1000 genomes] |
| rs28730510 | 0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs41272587 | 0.83[EUR][1000 genomes] |
| rs41272591 | 0.82[EUR][1000 genomes] |
| rs4282437 | 0.82[EUR][1000 genomes] |
| rs56307380 | 0.82[EUR][1000 genomes] |
| rs62407543 | 0.83[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs9348838 | 0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs9366754 | 0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes] |
| rs9378189 | 0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs9378221 | 0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs9380156 | 0.82[EUR][1000 genomes];0.82[ASN][1000 genomes] |
| rs9391677 | 0.83[EUR][1000 genomes];0.83[ASN][1000 genomes] |
| rs9391802 | 0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs9405046 | 0.84[EUR][1000 genomes];0.90[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv884058 | chr6:30182395-30202429 | Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 13 gene(s) | inside rSNPs | diseases |
| 2 | nsv884059 | chr6:30190484-30199016 | Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription | Chromatin interactive region | 1 gene(s) | inside rSNPs | diseases |
| 3 | nsv884060 | chr6:30190640-30203602 | Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS | TF binding regionChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs12660499 | TRIM26 | Cis_1M | lymphoblastoid | RTeQTL |
| rs12660499 | HCG18 | Cis_1M | lymphoblastoid | RTeQTL |
Chromatin state (count:0 , 50 per page) page:
| No data |
