Variant report
| Variant | rs4712804 |
|---|---|
| Chromosome Location | chr6:24163221-24163222 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:1)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:1 , 50 per page) page:
1
| No data |
(count:1 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr6:24156672..24158492-chr6:24162411..24164152,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000251830 | TF binding region |
rSNPs within LD-proxies of this variant (count:8)
| rs_ID | r2[population] |
|---|---|
| rs10946679 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs10946682 | 0.87[ASN][1000 genomes] |
| rs12211300 | 0.94[JPT][hapmap] |
| rs1417410 | 0.87[ASN][1000 genomes] |
| rs4607425 | 1.00[YRI][hapmap];0.93[AFR][1000 genomes] |
| rs4712803 | 0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs9348632 | 0.87[ASN][1000 genomes] |
| rs9393535 | 0.91[ASN][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 | nsv1029930 | chr6:23481989-24289948 | Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 13 gene(s) | inside rSNPs | diseases |
| 2 | esv1798372 | chr6:24158542-24181477 | Weak transcription Strong transcription Enhancers | TF binding regionCpG islandChromatin interactive region | 2 gene(s) | inside rSNPs | n/a |
mRNA abundance (count:9)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs4712804 | HIST1H3J | cis | cerebellum | SCAN |
| rs4712804 | CMAH | cis | parietal | SCAN |
| rs4712804 | HIST1H3G | cis | cerebellum | SCAN |
| rs4712804 | HIST1H2AK | cis | parietal | SCAN |
| rs4712804 | S100A2 | trans | parietal | SCAN |
| rs4712804 | HIST1H1D | cis | parietal | SCAN |
| rs4712804 | LOC284023 | trans | lymphoblastoid | RTeQTL |
| rs4712804 | HIST1H2AJ | cis | parietal | SCAN |
| rs4712804 | KAAG1 | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr6:24153800-24200800 | Weak transcription | H1 Derived Mesenchymal Stem Cells | ES cell derived |
