Variant report
| Variant | rs3114040 |
|---|---|
| Chromosome Location | chr4:127497536-127497537 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:4)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:4 , 50 per page) page:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr4:127496289..127499138-chr4:127502631..127504411,2 | K562 | blood: | |
| 2 | chr4:127495721..127499029-chr4:127500924..127504567,5 | K562 | blood: | |
| 3 | chr4:127493395..127495080-chr4:127497271..127498825,2 | K562 | blood: | |
| 4 | chr4:127489751..127491692-chr4:127495242..127497629,2 | K562 | blood: |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:16)
| rs_ID | r2[population] |
|---|---|
| rs1009241 | 0.89[EUR][1000 genomes];0.83[ASN][1000 genomes] |
| rs13112476 | 0.81[CEU][hapmap] |
| rs1511144 | 0.82[CEU][hapmap] |
| rs313087 | 0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes] |
| rs313095 | 0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs313096 | 0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes] |
| rs313097 | 0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes] |
| rs313098 | 0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs313105 | 0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes] |
| rs313144 | 0.94[EUR][1000 genomes] |
| rs313146 | 0.94[EUR][1000 genomes] |
| rs403001 | 0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs405317 | 0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs409435 | 0.84[AMR][1000 genomes];0.92[EUR][1000 genomes] |
| rs431286 | 0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs446534 | 0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:3 , 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 | nsv1012833 | chr4:127468474-127760933 | Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
| 2 | nsv537242 | chr4:127468474-127760933 | Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
| 3 | nsv524850 | chr4:127470903-127768849 | Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs3114040 | PLK4 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr4:127493800-127502200 | Weak transcription | K562 | blood |
