Variant report
| Variant | rs3922841 |
|---|---|
| Chromosome Location | chr6:25736678-25736679 |
| 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 | chr6:25726874..25732773-chr6:25733816..25737170,6 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000146047 | Chromatin interaction |
| ENSG00000178762 | Chromatin interaction |
| ENSG00000216436 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:4)
| rs_ID | r2[population] |
|---|---|
| rs12374627 | 0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs13190878 | 0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs9295669 | 0.92[CEU][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.86[EUR][1000 genomes] |
| rs9461211 | 0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page:
1
| 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 | nsv969355 | chr6:25733459-25779530 | Genic enhancers Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:10)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs3922841 | HIST1H2BM | cis | cerebellum | SCAN |
| rs3922841 | ZSCAN23 | cis | parietal | SCAN |
| rs3922841 | HIST1H2BH | cis | cerebellum | SCAN |
| rs3922841 | HIST1H4L | cis | cerebellum | SCAN |
| rs3922841 | HIST1H4E | cis | cerebellum | SCAN |
| rs3922841 | HIST1H4D | cis | cerebellum | SCAN |
| rs3922841 | HIST1H4C | cis | cerebellum | SCAN |
| rs3922841 | HIST1H4L | cis | parietal | SCAN |
| rs3922841 | ZSCAN23 | cis | cerebellum | SCAN |
| rs3922841 | HIST1H4F | cis | cerebellum | SCAN |
Chromatin state (count:0 , 50 per page) page:
| No data |
