Variant report
| Variant | rs3130116 |
|---|---|
| Chromosome Location | chr6:30365448-30365449 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:5)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:5 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr6:30325083..30325836-chr6:30364496..30366117,4 | MCF-7 | breast: | |
| 2 | chr6:30364759..30366950-chr6:30511934..30514120,2 | K562 | blood: | |
| 3 | chr6:30364310..30365862-chr6:30386384..30388997,2 | MCF-7 | breast: | |
| 4 | chr6:30325016..30326378-chr6:30364305..30365879,10 | K562 | blood: | |
| 5 | chr6:30332081..30333027-chr6:30364533..30365885,7 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:9)
| rs_ID | r2[population] |
|---|---|
| rs28994665 | 0.80[EUR][1000 genomes] |
| rs3094034 | 0.97[EUR][1000 genomes] |
| rs3094035 | 0.83[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs3094036 | 0.97[EUR][1000 genomes] |
| rs3094049 | 0.83[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs3094717 | 0.98[EUR][1000 genomes] |
| rs3131112 | 0.87[EUR][1000 genomes] |
| rs3132616 | 0.95[EUR][1000 genomes] |
| rs3132619 | 1.00[EUR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page:
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| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1025667 | chr6:30292845-30638066 | Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 825 gene(s) | inside rSNPs | diseases |
| 2 | nsv969293 | chr6:30348821-30368580 | Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription | Chromatin interactive region | 4 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:6)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs3130116 | ZNF192 | cis | parietal | SCAN |
| rs3130116 | HLA-C | Cis_1M | lymphoblastoid | RTeQTL |
| rs3130116 | HIST1H2BM | cis | cerebellum | SCAN |
| rs3130116 | HLA-A | cis | lymphoblastoid | GTEx |
| rs3130116 | ZNF323 | cis | parietal | SCAN |
| rs3130116 | ZKSCAN3 | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr6:30364800-30365600 | Bivalent Enhancer | iPS-15b Cell Line | embryonic stem cell |
