Variant report
| Variant | rs6419460 |
|---|---|
| Chromosome Location | chr1:209412567-209412568 |
| allele | A/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 | chr1:209412016..209414159-chr1:209416061..209418211,2 | K562 | blood: |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:21)
| rs_ID | r2[population] |
|---|---|
| rs10779504 | 0.91[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.85[EUR][1000 genomes] |
| rs10863764 | 0.85[AFR][1000 genomes] |
| rs10863765 | 0.87[EUR][1000 genomes];0.93[ASN][1000 genomes] |
| rs1354849 | 0.87[AFR][1000 genomes];0.87[EUR][1000 genomes] |
| rs1507334 | 0.87[AFR][1000 genomes];0.87[EUR][1000 genomes] |
| rs1933601 | 0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes] |
| rs2135817 | 0.93[AMR][1000 genomes];0.92[EUR][1000 genomes] |
| rs2250701 | 1.00[CHB][hapmap] |
| rs2660644 | 0.81[EUR][1000 genomes] |
| rs2788149 | 0.84[ASN][1000 genomes] |
| rs2788152 | 0.81[JPT][hapmap];0.81[MEX][hapmap] |
| rs2788154 | 0.84[ASN][1000 genomes] |
| rs2800916 | 0.86[ASN][1000 genomes] |
| rs2800934 | 0.84[ASN][1000 genomes] |
| rs4844466 | 0.85[AFR][1000 genomes] |
| rs6658956 | 1.00[CHB][hapmap] |
| rs6672407 | 1.00[CHB][hapmap] |
| rs6674807 | 0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs6690080 | 0.86[AFR][1000 genomes];0.87[EUR][1000 genomes] |
| rs6693967 | 0.87[AFR][1000 genomes];0.87[EUR][1000 genomes] |
| rs9943143 | 0.91[CEU][hapmap] |
Variant overlapped rSNPs/rCNVs (count:3 , 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 | nsv832481 | chr1:209371276-209540333 | Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 9 gene(s) | inside rSNPs | diseases |
| 2 | nsv832492 | chr1:209383771-209589312 | Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 9 gene(s) | inside rSNPs | diseases |
| 3 | esv1008555 | chr1:209409577-209416496 | Strong transcription Weak transcription Enhancers | Chromatin interactive region | n/a | inside rSNPs | diseases |
mRNA abundance (count:5)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs6419460 | CAMK1G | cis | cerebellum | SCAN |
| rs6419460 | SLC41A1 | cis | cerebellum | SCAN |
| rs6419460 | PPP1R15B | cis | cerebellum | SCAN |
| rs6419460 | ETNK2 | cis | cerebellum | SCAN |
| rs6419460 | YOD1 | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:209409800-209422200 | Weak transcription | Breast variant Human Mammary Epithelial Cells (vHMEC) | Breast |
