Variant report
| Variant | rs7723539 |
|---|---|
| Chromosome Location | chr5:44660210-44660211 |
| allele | C/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 | chr5:44659183..44661273-chr5:44664237..44666683,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:25)
| rs_ID | r2[population] |
|---|---|
| rs10805685 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs10805686 | 0.80[AMR][1000 genomes];0.99[EUR][1000 genomes] |
| rs10941677 | 0.98[EUR][1000 genomes] |
| rs12516900 | 0.95[EUR][1000 genomes] |
| rs12522626 | 0.80[AMR][1000 genomes];0.95[EUR][1000 genomes] |
| rs2013513 | 1.00[CEU][hapmap] |
| rs2218080 | 0.92[CEU][hapmap] |
| rs2218081 | 1.00[CEU][hapmap] |
| rs36068815 | 0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes] |
| rs4321755 | 0.95[EUR][1000 genomes] |
| rs4415084 | 0.98[EUR][1000 genomes] |
| rs4415085 | 0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs4463188 | 0.95[EUR][1000 genomes] |
| rs4479849 | 0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes] |
| rs4492118 | 0.95[EUR][1000 genomes] |
| rs4571480 | 0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs4571481 | 0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs66996829 | 0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs6890556 | 0.96[EUR][1000 genomes] |
| rs714130 | 1.00[CEU][hapmap] |
| rs7701466 | 0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs7720551 | 0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs7735881 | 0.94[EUR][1000 genomes] |
| rs920329 | 1.00[CEU][hapmap] |
| rs930395 | 0.82[CHB][hapmap] |
Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv830278 | chr5:44540863-44713312 | Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 6 gene(s) | inside rSNPs | diseases |
| 2 | nsv537742 | chr5:44620084-44664039 | Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats | Chromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | n/a |
| 3 | nsv880457 | chr5:44632008-44800665 | Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 7 gene(s) | inside rSNPs | diseases |
| 4 | esv3450647 | chr5:44660177-44660482 | Enhancers | Chromatin interactive region | n/a | inside rSNPs | n/a |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs7723539 | LOC647121 | Cis_chr | lymphoblastoid | RTeQTL |
| rs7723539 | RP11-53O19.3 | cis | Nerve Tibial | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr5:44657800-44662200 | Enhancers | H9 Derived Neuron Cultured Cells | ES cell derived |
| 2 | chr5:44658400-44661000 | Enhancers | H9 Derived Neuronal Progenitor Cultured Cells | ES cell derived |
| 3 | chr5:44659000-44661600 | Enhancers | Adipose Derived Mesenchymal Stem Cell Cultured Cells | ES cell derived |
