Variant report
| Variant | rs879738 |
|---|---|
| Chromosome Location | chr5:79621016-79621017 |
| allele | A/G |
| 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:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr2:46228..48236-chr5:79619683..79622424,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000184731 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:13)
| rs_ID | r2[population] |
|---|---|
| rs10037935 | 0.90[JPT][hapmap] |
| rs12055120 | 0.80[JPT][hapmap] |
| rs12651951 | 0.82[JPT][hapmap] |
| rs12654489 | 0.81[JPT][hapmap] |
| rs13160125 | 0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[ASN][1000 genomes] |
| rs13179066 | 0.80[JPT][hapmap] |
| rs1990858 | 0.98[ASN][1000 genomes] |
| rs2405378 | 0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs4704663 | 0.81[ASN][1000 genomes] |
| rs6866850 | 0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[ASN][1000 genomes] |
| rs6876442 | 0.82[JPT][hapmap] |
| rs73113892 | 0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs9293816 | 0.81[JPT][hapmap] |
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 |
|---|---|---|---|---|
| rs879738 | SERINC5 | cis | parietal | SCAN |
| rs879738 | AP3B1 | cis | cerebellum | SCAN |
Chromatin state (count:0 , 50 per page) page:
| No data |
