Variant report
| Variant | rs8053720 |
|---|---|
| Chromosome Location | chr16:71456142-71456143 |
| 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 | chr16:71446373..71446879-chr16:71455612..71456584,2 | K562 | blood: | |
| 2 | chr16:71446325..71447209-chr16:71455576..71456210,4 | MCF-7 | breast: | |
| 3 | chr16:71400996..71401584-chr16:71455562..71456517,2 | K562 | blood: | |
| 4 | chr16:71455740..71456643-chr16:71466049..71466727,2 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000260734 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:18)
| rs_ID | r2[population] |
|---|---|
| rs10500562 | 0.81[CEU][hapmap] |
| rs12447033 | 0.81[CEU][hapmap];0.90[MEX][hapmap] |
| rs12708914 | 0.80[EUR][1000 genomes] |
| rs12919417 | 0.90[MEX][hapmap] |
| rs12922775 | 0.81[CEU][hapmap] |
| rs12927006 | 0.90[CEU][hapmap] |
| rs12927456 | 0.90[CEU][hapmap] |
| rs12931191 | 0.81[CEU][hapmap];0.90[MEX][hapmap] |
| rs17280181 | 1.00[CEU][hapmap] |
| rs17345863 | 0.88[CEU][hapmap] |
| rs17347255 | 0.81[CEU][hapmap] |
| rs56893224 | 1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes] |
| rs71403847 | 0.84[AMR][1000 genomes];0.80[EUR][1000 genomes] |
| rs71403849 | 0.86[AMR][1000 genomes] |
| rs7195767 | 0.93[AMR][1000 genomes];0.80[EUR][1000 genomes] |
| rs7203606 | 0.81[CEU][hapmap];0.90[MEX][hapmap] |
| rs8051974 | 0.91[ASW][hapmap];0.90[CEU][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes] |
| rs8063455 | 0.81[CEU][hapmap];0.90[MEX][hapmap] |
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 | nsv949461 | chr16:71196153-71579711 | ZNF genes & repeats Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 41 gene(s) | inside rSNPs | diseases |
| 2 | nsv1064435 | chr16:71440719-71488771 | Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 9 gene(s) | inside rSNPs | diseases |
| 3 | nsv977998 | chr16:71454098-71457409 | Weak transcription Enhancers Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:6)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs8053720 | CTRL | cis | cerebellum | SCAN |
| rs8053720 | CMTM2 | cis | parietal | SCAN |
| rs8053720 | ATP6V0D1 | cis | parietal | SCAN |
| rs8053720 | FAM65A | cis | cerebellum | SCAN |
| rs8053720 | NRN1L | cis | parietal | SCAN |
| rs8053720 | HP | cis | multi-tissue | Pritchard |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr16:71446800-71459600 | Weak transcription | Spleen | Spleen |
| 2 | chr16:71455800-71458800 | Weak transcription | iPS DF 19.11 Cell Line | embryonic stem cell |
