Variant report
| Variant | rs6712004 |
|---|---|
| Chromosome Location | chr2:12110926-12110927 |
| 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 | chr2:12109181..12111503-chr2:12144590..12147302,2 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000224184 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:14)
| rs_ID | r2[population] |
|---|---|
| rs10460294 | 0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs10929774 | 0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs11694407 | 0.84[EUR][1000 genomes] |
| rs11695533 | 0.81[ASN][1000 genomes] |
| rs12989918 | 0.90[EUR][1000 genomes] |
| rs13003327 | 0.91[CEU][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes] |
| rs13003710 | 0.83[JPT][hapmap];0.84[ASN][1000 genomes] |
| rs13015144 | 0.84[ASN][1000 genomes] |
| rs13019206 | 0.86[EUR][1000 genomes];0.83[ASN][1000 genomes] |
| rs13020034 | 0.84[ASN][1000 genomes] |
| rs1595807 | 1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs6709058 | 0.87[YRI][hapmap] |
| rs7575078 | 0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs972873 | 0.90[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 | nsv1003899 | chr2:11789374-12248081 | Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA | 26 gene(s) | inside rSNPs | diseases |
| 2 | nsv833403 | chr2:11944552-12125634 | Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA | 10 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs6712004 | KCNF1 | cis | cerebellum | SCAN |
| rs6712004 | IAH1 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr2:12110600-12111000 | Genic enhancers | Breast variant Human Mammary Epithelial Cells (vHMEC) | Breast |
