Variant report
| Variant | rs9304727 |
|---|---|
| Chromosome Location | chr19:52768097-52768098 |
| 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 | chr19:52765891..52768677-chr19:52771082..52773186,3 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000196214 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:13)
| rs_ID | r2[population] |
|---|---|
| rs10410891 | 0.80[AMR][1000 genomes];0.81[EUR][1000 genomes] |
| rs10426950 | 0.93[AFR][1000 genomes];0.95[ASN][1000 genomes] |
| rs2560875 | 0.90[AFR][1000 genomes] |
| rs2560877 | 0.81[MKK][hapmap] |
| rs2657924 | 0.82[YRI][hapmap] |
| rs2657926 | 0.82[YRI][hapmap] |
| rs2657927 | 0.84[AFR][1000 genomes] |
| rs2657928 | 0.90[AFR][1000 genomes] |
| rs2657930 | 0.83[LWK][hapmap];0.84[MKK][hapmap];0.89[YRI][hapmap] |
| rs4802914 | 0.85[JPT][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs6509630 | 0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs8112349 | 0.83[AFR][1000 genomes];0.91[ASN][1000 genomes] |
| rs9304725 | 0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1065410 | chr19:52103914-52889530 | Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 596 gene(s) | inside rSNPs | diseases |
| 2 | esv3366000 | chr19:52491073-52842946 | Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 48 gene(s) | inside rSNPs | diseases |
| 3 | nsv1066015 | chr19:52502213-52890308 | Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 49 gene(s) | inside rSNPs | diseases |
| 4 | nsv544059 | chr19:52502213-52890308 | Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 49 gene(s) | inside rSNPs | diseases |
| 5 | nsv517598 | chr19:52768097-52768432 | Weak transcription | Chromatin interactive region | 1 gene(s) | inside rSNPs | n/a |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs9304727 | ZNF132 | cis | parietal | SCAN |
| rs9304727 | GP6 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr19:52758600-52772200 | Weak transcription | Stomach Smooth Muscle | stomach |
| 2 | chr19:52763400-52772200 | Weak transcription | Placenta | Placenta |
