Variant report
| Variant | rs2876673 |
|---|---|
| Chromosome Location | chr6:24738595-24738596 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:6)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:6 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr6:24736323..24738975-chr6:24757709..24759492,2 | K562 | blood: | |
| 2 | chr6:24735312..24737192-chr6:24737819..24739636,2 | K562 | blood: | |
| 3 | chr6:24720377..24722365-chr6:24737206..24739531,2 | MCF-7 | breast: | |
| 4 | chr6:24719100..24724705-chr6:24735495..24739885,7 | K562 | blood: | |
| 5 | chr6:24738046..24740803-chr6:24741877..24743949,2 | K562 | blood: | |
| 6 | chr6:24738215..24741096-chr6:24774621..24776163,2 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000224164 | Chromatin interaction |
| ENSG00000112312 | Chromatin interaction |
| ENSG00000112308 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:12)
| rs_ID | r2[population] |
|---|---|
| rs10806992 | 0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs2038541 | 0.92[AFR][1000 genomes];0.99[ASN][1000 genomes] |
| rs2064977 | 0.84[ASN][1000 genomes] |
| rs2145753 | 0.82[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes] |
| rs2294686 | 0.81[JPT][hapmap] |
| rs4712841 | 0.82[ASN][1000 genomes] |
| rs4712843 | 0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs7762810 | 0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs9356944 | 0.81[JPT][hapmap] |
| rs9356945 | 1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs9379686 | 0.81[JPT][hapmap] |
| rs9393585 | 0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[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 | nsv830609 | chr6:24712086-24896647 | Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 68 gene(s) | inside rSNPs | diseases |
| 2 | nsv428474 | chr6:24714157-24797977 | Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 65 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:4)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs2876673 | HIST1H4F | cis | cerebellum | SCAN |
| rs2876673 | SLC17A1 | cis | parietal | SCAN |
| rs2876673 | OR2B2 | cis | parietal | SCAN |
| rs2876673 | HIST1H1D | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr6:24737000-24738800 | Weak transcription | Stomach Mucosa | stomach |
