Variant report
| Variant | rs1233582 |
|---|---|
| Chromosome Location | chr6:28714044-28714045 |
| allele | C/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:4)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:4 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr6:28685695..28690739-chr6:28709794..28719692,17 | K562 | blood: | |
| 2 | chr6:28683304..28685259-chr6:28712068..28714540,2 | MCF-7 | breast: | |
| 3 | chr6:28711220..28714517-chr6:28890097..28893318,3 | K562 | blood: | |
| 4 | chr6:28712043..28717130-chr6:28723838..28729658,8 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000204713 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:35)
| rs_ID | r2[population] |
|---|---|
| rs10498733 | 0.93[ASN][1000 genomes] |
| rs1233597 | 0.83[AFR][1000 genomes] |
| rs1233614 | 0.86[AFR][1000 genomes];0.86[AMR][1000 genomes] |
| rs17280797 | 0.96[ASN][1000 genomes] |
| rs17280818 | 1.00[ASN][1000 genomes] |
| rs17281186 | 1.00[ASN][1000 genomes] |
| rs17346574 | 0.96[ASN][1000 genomes] |
| rs17398081 | 0.81[ASN][1000 genomes] |
| rs1742741 | 0.81[AFR][1000 genomes] |
| rs1936180 | 0.93[ASN][1000 genomes] |
| rs2765220 | 0.81[AMR][1000 genomes] |
| rs3132372 | 0.81[AMR][1000 genomes] |
| rs417919 | 0.81[AMR][1000 genomes] |
| rs55641015 | 0.81[ASN][1000 genomes] |
| rs55891766 | 1.00[ASN][1000 genomes] |
| rs57170714 | 0.81[ASN][1000 genomes] |
| rs58104924 | 0.93[ASN][1000 genomes] |
| rs59233561 | 0.81[ASN][1000 genomes] |
| rs59475656 | 0.81[ASN][1000 genomes] |
| rs59959723 | 1.00[ASN][1000 genomes] |
| rs60311527 | 0.88[ASN][1000 genomes] |
| rs61094745 | 1.00[ASN][1000 genomes] |
| rs61703239 | 0.81[ASN][1000 genomes] |
| rs7742889 | 0.81[ASN][1000 genomes] |
| rs7748319 | 0.96[ASN][1000 genomes] |
| rs7751884 | 0.84[ASN][1000 genomes] |
| rs7755641 | 0.93[ASN][1000 genomes] |
| rs7760656 | 1.00[ASN][1000 genomes] |
| rs7765829 | 1.00[ASN][1000 genomes] |
| rs7766599 | 1.00[ASN][1000 genomes] |
| rs7772111 | 0.88[ASN][1000 genomes] |
| rs7772682 | 0.88[ASN][1000 genomes] |
| rs9257182 | 0.81[AFR][1000 genomes];0.86[AMR][1000 genomes] |
| rs9257190 | 0.96[AMR][1000 genomes];0.85[EUR][1000 genomes] |
| rs9257226 | 0.81[AMR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv534089 | chr6:28636972-28841640 | Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 43 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:3)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs1233582 | BTN3A2 | Cis_chr | lymphoblastoid | RTeQTL |
| rs1233582 | BTN3A2///BTN3A3 | Cis_chr | lymphoblastoid | RTeQTL |
| rs1233582 | ZFP57 | Cis_1M | lymphoblastoid | RTeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr6:28712000-28714200 | Weak transcription | A549 | lung |
| 2 | chr6:28712200-28714200 | Weak transcription | K562 | blood |
