Variant report
| Variant | rs56862318 |
|---|---|
| Chromosome Location | chr6:27185354-27185355 |
| 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 | chr6:27182916..27186403-chr6:27189146..27192783,3 | K562 | blood: |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:6)
| rs_ID | r2[population] |
|---|---|
| rs13212921 | 0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes] |
| rs13219354 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs34817112 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs35909544 | 0.95[AFR][1000 genomes];0.99[EUR][1000 genomes] |
| rs4452638 | 0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes] |
| rs67457459 | 0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes] |
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 | nsv948921 | chr6:26556890-27443957 | Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 472 gene(s) | inside rSNPs | diseases |
| 2 | nsv1017328 | chr6:27177147-27369588 | Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 29 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:11)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs56862318 | BTN3A2 | cis | lung | GTEx |
| rs56862318 | BTN3A2 | cis | Muscle Skeletal | GTEx |
| rs56862318 | BTN3A2///BTN3A3 | Cis_1M | lymphoblastoid | RTeQTL |
| rs56862318 | BTN3A2 | cis | Thyroid | GTEx |
| rs56862318 | BTN3A2 | cis | Adipose Subcutaneous | GTEx |
| rs56862318 | BTN3A2 | Cis_1M | lymphoblastoid | RTeQTL |
| rs56862318 | BTN3A2 | cis | Esophagus Muscularis | GTEx |
| rs56862318 | BTN3A2 | cis | Skin Sun Exposed Lower leg | GTEx |
| rs56862318 | BTN3A2 | cis | Whole Blood | GTEx |
| rs56862318 | BTN3A2 | cis | Nerve Tibial | GTEx |
| rs56862318 | BTN3A2 | cis | Esophagus Mucosa | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr6:27183000-27197200 | Weak transcription | iPS DF 19.11 Cell Line | embryonic stem cell |
