Variant report
| Variant | rs28360585 |
|---|---|
| Chromosome Location | chr6:25790356-25790357 |
| allele | A/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:2)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
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(count:2 , 50 per page) page:
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| No data |
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rSNPs within LD-proxies of this variant (count:23)
| rs_ID | r2[population] |
|---|---|
| rs10214468 | 0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs1165184 | 0.82[EUR][1000 genomes] |
| rs13193685 | 0.83[AFR][1000 genomes];0.87[ASN][1000 genomes] |
| rs1324082 | 0.90[AFR][1000 genomes];0.87[ASN][1000 genomes] |
| rs1324087 | 0.86[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs1324088 | 0.86[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs1575534 | 0.89[AFR][1000 genomes];0.87[ASN][1000 genomes] |
| rs1924469 | 0.89[AFR][1000 genomes];0.87[ASN][1000 genomes] |
| rs1951905 | 0.89[AFR][1000 genomes];0.87[ASN][1000 genomes] |
| rs3799346 | 0.90[AFR][1000 genomes];0.87[ASN][1000 genomes] |
| rs3799350 | 0.92[AFR][1000 genomes];0.87[ASN][1000 genomes] |
| rs3823151 | 0.86[ASN][1000 genomes] |
| rs56777435 | 0.86[ASN][1000 genomes] |
| rs58366507 | 0.86[ASN][1000 genomes] |
| rs6913879 | 0.83[AFR][1000 genomes];0.83[ASN][1000 genomes] |
| rs7753366 | 0.83[AFR][1000 genomes];0.83[ASN][1000 genomes] |
| rs942377 | 0.92[AFR][1000 genomes];0.87[ASN][1000 genomes] |
| rs942378 | 0.89[AFR][1000 genomes];0.87[ASN][1000 genomes] |
| rs9461215 | 0.89[AFR][1000 genomes];0.85[ASN][1000 genomes] |
| rs9467604 | 0.87[AFR][1000 genomes];0.87[ASN][1000 genomes] |
| rs9467610 | 0.89[AFR][1000 genomes];0.87[ASN][1000 genomes] |
| rs9467614 | 0.88[AFR][1000 genomes];0.87[ASN][1000 genomes] |
| rs9467615 | 0.88[AFR][1000 genomes];0.87[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:4 , 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 | nsv1029920 | chr6:25638507-26585842 | Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 1215 gene(s) | inside rSNPs | diseases |
| 2 | nsv538162 | chr6:25638507-26585842 | Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 1215 gene(s) | inside rSNPs | diseases |
| 3 | nsv427747 | chr6:25641380-25908218 | Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 21 gene(s) | inside rSNPs | diseases |
| 4 | nsv883489 | chr6:25789061-25821770 | Strong transcription Enhancers Weak transcription | Chromatin interactive regionlncRNA | 5 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs28360585 | BTN3A2 | Cis_1M | lymphoblastoid | RTeQTL |
| rs28360585 | BTN3A2///BTN3A3 | Cis_1M | lymphoblastoid | RTeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr6:25780400-25798800 | Weak transcription | Liver | Liver |
| 2 | chr6:25787600-25790600 | Enhancers | Foreskin Melanocyte Primary Cells skin03 | Skin |
