Variant report
| Variant | rs478526 |
|---|---|
| Chromosome Location | chr1:47991951-47991952 |
| allele | A/C |
| 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 | chr1:47990094..47992999-chr1:47995036..47996559,2 | K562 | blood: |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:22)
| rs_ID | r2[population] |
|---|---|
| rs1024108 | 0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs11585530 | 0.94[CEU][hapmap];0.92[EUR][1000 genomes] |
| rs11799997 | 0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs17103342 | 0.94[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes] |
| rs17103383 | 0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs2102437 | 0.92[EUR][1000 genomes] |
| rs28493519 | 0.83[EUR][1000 genomes] |
| rs471608 | 0.93[EUR][1000 genomes] |
| rs560540 | 0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs56404532 | 0.80[AMR][1000 genomes];0.94[EUR][1000 genomes] |
| rs578335 | 0.93[EUR][1000 genomes] |
| rs59326446 | 0.80[AMR][1000 genomes];0.94[EUR][1000 genomes] |
| rs59865928 | 0.93[EUR][1000 genomes] |
| rs60503680 | 0.93[EUR][1000 genomes] |
| rs635710 | 0.93[EUR][1000 genomes] |
| rs6681140 | 0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs6688849 | 0.93[EUR][1000 genomes] |
| rs72904553 | 0.86[EUR][1000 genomes] |
| rs72904554 | 0.86[EUR][1000 genomes] |
| rs7531586 | 0.82[AMR][1000 genomes];0.94[EUR][1000 genomes] |
| rs7543243 | 0.87[EUR][1000 genomes] |
| rs822886 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1001779 | chr1:47884229-48111485 | Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 18 gene(s) | inside rSNPs | diseases |
| 2 | nsv871299 | chr1:47889417-48057890 | Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 17 gene(s) | inside rSNPs | diseases |
| 3 | esv2755190 | chr1:47907580-48048680 | Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 10 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:3)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs478526 | CDKN2C | cis | parietal | SCAN |
| rs478526 | MAST2 | cis | cerebellum | SCAN |
| rs478526 | IPP | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:47991000-47992200 | Weak transcription | hESC Derived CD184+ Endoderm Cultured Cells | ES cell derived |
| 2 | chr1:47991000-47993200 | Weak transcription | Liver | Liver |
