Variant report
| Variant | rs1064319 |
|---|---|
| Chromosome Location | chr12:119866533-119866534 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:1)
- 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 | chr12:119861971..119864906-chr12:119864949..119866973,2 | K562 | blood: |
(count:1 , 50 per page) page:
1
| No. | lncRNA name | Chromosome Location | lncRNA alias |
|---|---|---|---|
| 1 | lnc-HSPB8-7 | chr12:119866488-119866567 | NONHSAT031079 |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:14)
| rs_ID | r2[population] |
|---|---|
| rs11064794 | 0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs1520760 | 0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes] |
| rs1620795 | 0.98[ASN][1000 genomes] |
| rs1716467 | 1.00[ASN][1000 genomes] |
| rs1716469 | 1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes] |
| rs1716470 | 1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes] |
| rs1716471 | 1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes] |
| rs1727386 | 0.99[ASN][1000 genomes] |
| rs1727388 | 1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes] |
| rs4766942 | 1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs7306893 | 0.99[ASN][1000 genomes] |
| rs784859 | 0.95[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap] |
| rs884034 | 0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes] |
| rs953693 | 0.90[GIH][hapmap] |
Variant overlapped rSNPs/rCNVs (count:4 , 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 | nsv1047036 | chr12:119477583-119992640 | Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 15 gene(s) | inside rSNPs | diseases |
| 2 | nsv916688 | chr12:119801814-120044407 | Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 8 gene(s) | inside rSNPs | diseases |
| 3 | nsv899553 | chr12:119837250-119876571 | Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats | Chromatin interactive regionlncRNA | 1 gene(s) | inside rSNPs | diseases |
| 4 | nsv832529 | chr12:119863378-120071646 | Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 8 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs1064319 | VSIG10 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr12:119851600-119872400 | Weak transcription | iPS DF 19.11 Cell Line | embryonic stem cell |
