Variant report
| Variant | rs13333985 |
|---|---|
| Chromosome Location | chr16:71550853-71550854 |
| allele | C/T |
| 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 | chr16:71517067..71518661-chr16:71548978..71551457,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000157429 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:15)
| rs_ID | r2[population] |
|---|---|
| rs11866859 | 0.96[CEU][hapmap];0.88[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes] |
| rs12935725 | 0.95[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs16972663 | 0.91[CEU][hapmap];0.85[EUR][1000 genomes] |
| rs16972805 | 0.96[CEU][hapmap];0.88[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes] |
| rs310335 | 0.96[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs4258624 | 0.96[CEU][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes] |
| rs4644867 | 0.85[EUR][1000 genomes] |
| rs59364668 | 1.00[ASN][1000 genomes] |
| rs7184543 | 0.88[YRI][hapmap] |
| rs7188475 | 0.92[CEU][hapmap];0.84[TSI][hapmap] |
| rs7188858 | 0.84[EUR][1000 genomes] |
| rs7199026 | 0.88[YRI][hapmap] |
| rs7499392 | 0.84[EUR][1000 genomes] |
| rs8044068 | 0.81[AFR][1000 genomes] |
| rs9940485 | 0.93[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 | 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 | nsv906892 | chr16:71526720-71570413 | Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 9 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:7)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs13333985 | CMTM1 | cis | cerebellum | SCAN |
| rs13333985 | TPPP3 | cis | cerebellum | SCAN |
| rs13333985 | ZNF23 | cis | parietal | SCAN |
| rs13333985 | ATP6V0D1 | cis | parietal | SCAN |
| rs13333985 | SNTB2 | cis | cerebellum | SCAN |
| rs13333985 | CBFB | cis | parietal | SCAN |
| rs13333985 | HSF4 | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr16:71549200-71558400 | Weak transcription | ES-I3 Cell Line | embryonic stem cell |
| 2 | chr16:71549800-71551200 | Enhancers | Pancreas | Pancrea |
