Variant report
| Variant | rs4428437 |
|---|---|
| Chromosome Location | chr5:164456692-164456693 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:5)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:5 , 50 per page) page:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr5:164456273..164457115-chr5:164635699..164636841,5 | MCF-7 | breast: | |
| 2 | chr5:164456280..164457191-chr5:164635732..164636716,3 | MCF-7 | breast: | |
| 3 | chr5:163439449..163440316-chr5:164456391..164457131,2 | MCF-7 | breast: | |
| 4 | chr5:164456268..164457507-chr5:164884675..164886184,4 | MCF-7 | breast: | |
| 5 | chr5:164456344..164456958-chr5:164924436..164925021,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:8)
| rs_ID | r2[population] |
|---|---|
| rs11135339 | 0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs13153549 | 0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs4327610 | 0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs6556790 | 0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs6556791 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs6870981 | 0.87[AFR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes] |
| rs6872152 | 0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs7714848 | 0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page:
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| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv995060 | chr5:163660200-164620500 | Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 11 gene(s) | inside rSNPs | diseases |
| 2 | nsv528624 | chr5:164319435-164701201 | Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
| 3 | nsv600242 | chr5:164391457-164466785 | Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS | TF binding regionChromatin interactive regionlncRNA | 1 gene(s) | inside rSNPs | diseases |
| 4 | nsv1033866 | chr5:164419608-164677758 | Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 1 gene(s) | inside rSNPs | diseases |
| 5 | nsv883092 | chr5:164443094-164529549 | Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS | Chromatin interactive region | n/a | inside rSNPs | diseases |
| 6 | nsv1031772 | chr5:164451602-164512911 | Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats | Chromatin interactive region | n/a | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs4428437 | GABRB2 | cis | parietal | SCAN |
| rs4428437 | WWC1 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr5:164452400-164457000 | Weak transcription | Primary hematopoietic stem cells short term culture | blood |
