Variant report
| Variant | rs7301599 |
|---|---|
| Chromosome Location | chr12:119853272-119853273 |
| allele | G/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
| No data |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:24)
| rs_ID | r2[population] |
|---|---|
| rs10774496 | 0.93[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap] |
| rs10849647 | 0.93[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap] |
| rs10849651 | 0.93[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap] |
| rs10849652 | 0.93[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap] |
| rs10849654 | 0.87[ASN][1000 genomes] |
| rs10849656 | 0.93[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes] |
| rs10849657 | 1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes] |
| rs10849658 | 0.90[ASN][1000 genomes] |
| rs10849659 | 1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes] |
| rs11064761 | 0.88[CHB][hapmap] |
| rs11064763 | 0.93[CHB][hapmap];0.95[JPT][hapmap] |
| rs11064764 | 0.93[CHB][hapmap];0.95[JPT][hapmap] |
| rs11064790 | 0.80[CEU][hapmap];0.95[TSI][hapmap] |
| rs12370130 | 0.90[CHD][hapmap] |
| rs34765258 | 0.94[ASN][1000 genomes] |
| rs4300442 | 0.93[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes] |
| rs4346024 | 0.90[ASN][1000 genomes] |
| rs4384428 | 0.96[CEU][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes] |
| rs4465416 | 1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes] |
| rs4991185 | 0.93[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes] |
| rs7132771 | 0.84[EUR][1000 genomes] |
| rs7298161 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs7313792 | 1.00[CHB][hapmap];0.90[JPT][hapmap] |
| rs7485706 | 0.80[CEU][hapmap];0.95[TSI][hapmap];0.81[EUR][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 | 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 |
mRNA abundance (count:4)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs7301599 | ACADS | cis | parietal | SCAN |
| rs7301599 | RNF10 | cis | cerebellum | SCAN |
| rs7301599 | SIRT4 | cis | cerebellum | SCAN |
| rs7301599 | FBXW8 | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr12:119851600-119872400 | Weak transcription | iPS DF 19.11 Cell Line | embryonic stem cell |
| 2 | chr12:119853000-119853600 | Enhancers | Placenta | Placenta |
| 3 | chr12:119853000-119853600 | Enhancers | Rectal Mucosa Donor 31 | rectum |
