Variant report
| Variant | rs3094561 |
|---|---|
| Chromosome Location | chr6:29404157-29404158 |
| allele | A/C |
| 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:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr6:29403021..29405389-chr6:29406717..29409334,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000206474 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:15)
| rs_ID | r2[population] |
|---|---|
| rs1362075 | 0.81[EUR][1000 genomes] |
| rs1592412 | 0.81[EUR][1000 genomes] |
| rs2074464 | 0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs2107191 | 0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs3094564 | 0.80[EUR][1000 genomes] |
| rs3094572 | 0.81[EUR][1000 genomes] |
| rs3094573 | 0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs3094574 | 0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs3117194 | 0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs3128844 | 0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs3128854 | 0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs3130852 | 0.81[EUR][1000 genomes] |
| rs3130854 | 0.80[EUR][1000 genomes] |
| rs3131019 | 0.81[EUR][1000 genomes] |
| rs734959 | 0.81[EUR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv830624 | chr6:29274525-29445565 | Enhancers Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 11 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:3)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs3094561 | ZFP57 | Cis_1M | lymphoblastoid | RTeQTL |
| rs3094561 | ZKSCAN3 | cis | cerebellum | SCAN |
| rs3094561 | SLC17A3 | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr6:29403800-29404200 | Enhancers | HepG2 | liver |
