Variant report
| Variant | rs10070958 |
|---|---|
| Chromosome Location | chr5:79588679-79588680 |
| 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:32)
| rs_ID | r2[population] |
|---|---|
| rs10041270 | 0.81[JPT][hapmap] |
| rs10052506 | 0.86[ASN][1000 genomes] |
| rs10054681 | 0.96[ASN][1000 genomes] |
| rs10054927 | 0.87[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes] |
| rs10055300 | 0.96[ASN][1000 genomes] |
| rs10056958 | 1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.96[ASN][1000 genomes] |
| rs10070311 | 0.95[ASN][1000 genomes] |
| rs10071189 | 0.97[AFR][1000 genomes];0.96[ASN][1000 genomes] |
| rs10075519 | 0.91[ASN][1000 genomes] |
| rs10474013 | 0.80[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs10474015 | 0.94[ASN][1000 genomes] |
| rs10474614 | 0.90[AFR][1000 genomes];0.96[ASN][1000 genomes] |
| rs1126176 | 0.82[JPT][hapmap] |
| rs12332228 | 0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs12332699 | 1.00[ASN][1000 genomes] |
| rs13361029 | 0.90[AFR][1000 genomes];0.96[ASN][1000 genomes] |
| rs28366631 | 1.00[ASN][1000 genomes] |
| rs28401747 | 1.00[ASN][1000 genomes] |
| rs28424275 | 0.97[AFR][1000 genomes];1.00[ASN][1000 genomes] |
| rs28520641 | 0.88[ASN][1000 genomes] |
| rs28605690 | 0.90[ASN][1000 genomes] |
| rs6453512 | 0.96[ASN][1000 genomes] |
| rs6872359 | 0.82[JPT][hapmap] |
| rs72778013 | 0.90[AFR][1000 genomes];0.96[ASN][1000 genomes] |
| rs72778033 | 1.00[ASN][1000 genomes] |
| rs72778039 | 0.88[ASN][1000 genomes] |
| rs9293807 | 0.82[JPT][hapmap] |
| rs9293808 | 0.81[JPT][hapmap] |
| rs9293811 | 0.97[AFR][1000 genomes];0.99[ASN][1000 genomes] |
| rs9293814 | 0.82[ASN][1000 genomes] |
| rs950788 | 0.96[ASN][1000 genomes] |
| rs9654436 | 0.90[AFR][1000 genomes];0.96[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv948807 | chr5:79549207-79805765 | Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 49 gene(s) | inside rSNPs | diseases |
| 2 | nsv518480 | chr5:79586085-79748382 | Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 26 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs10070958 | SERINC5 | cis | parietal | SCAN |
| rs10070958 | MSH3 | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr5:79580600-79595400 | Weak transcription | iPS DF 19.11 Cell Line | embryonic stem cell |
