Variant report
| Variant | rs6917087 |
|---|---|
| Chromosome Location | chr6:56298479-56298480 |
| 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:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr6:56298331..56299890-chr6:56404895..56406980,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000151914 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:14)
| rs_ID | r2[population] |
|---|---|
| rs10484787 | 1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes] |
| rs12195424 | 0.81[AFR][1000 genomes];0.81[AMR][1000 genomes] |
| rs1323318 | 1.00[CEU][hapmap];0.96[EUR][1000 genomes] |
| rs1323319 | 1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes] |
| rs16887916 | 0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes] |
| rs2209037 | 1.00[CEU][hapmap];0.96[EUR][1000 genomes] |
| rs2224749 | 1.00[CEU][hapmap];0.96[EUR][1000 genomes] |
| rs2397225 | 0.92[AFR][1000 genomes];0.84[AMR][1000 genomes] |
| rs6903211 | 0.85[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap] |
| rs6915066 | 1.00[CEU][hapmap];0.96[EUR][1000 genomes] |
| rs6941846 | 0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs73465822 | 0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs9475698 | 1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs9475702 | 1.00[JPT][hapmap] |
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 | nsv491933 | chr6:56177722-57171010 | Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 51 gene(s) | inside rSNPs | diseases |
| 2 | nsv830666 | chr6:56243743-56419599 | Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 9 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs6917087 | COL21A1 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr6:56298400-56299600 | Weak transcription | Fetal Intestine Large | intestine |
