Variant report
| Variant | rs1400216 |
|---|---|
| Chromosome Location | chr15:58398602-58398603 |
| 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 | chr15:58369470..58372316-chr15:58397826..58400720,3 | K562 | blood: |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:9)
| rs_ID | r2[population] |
|---|---|
| rs12906402 | 0.80[TSI][hapmap] |
| rs12909201 | 0.81[EUR][1000 genomes] |
| rs1516400 | 0.82[MEX][hapmap] |
| rs1516401 | 0.84[CEU][hapmap];0.83[CHB][hapmap];0.95[EUR][1000 genomes] |
| rs1874159 | 0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes] |
| rs2642629 | 0.88[CEU][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes] |
| rs2642647 | 0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs2704206 | 0.86[AMR][1000 genomes];0.95[EUR][1000 genomes] |
| rs2704237 | 0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1038667 | chr15:57933076-58481870 | Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 22 gene(s) | inside rSNPs | diseases |
| 2 | nsv542400 | chr15:57933076-58481870 | Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 22 gene(s) | inside rSNPs | diseases |
| 3 | nsv904263 | chr15:58340072-58437346 | Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 8 gene(s) | inside rSNPs | diseases |
| 4 | nsv569596 | chr15:58355798-58408763 | Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 7 gene(s) | inside rSNPs | diseases |
| 5 | nsv1047246 | chr15:58375607-58707158 | Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 18 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs1400216 | TCF12 | cis | cerebellum | SCAN |
| rs1400216 | LOC654342 | trans | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr15:58398600-58400200 | Enhancers | K562 | blood |
