Variant report
| Variant | rs34664345 |
|---|---|
| Chromosome Location | chr14:39691728-39691729 |
| allele | A/G |
| 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:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr14:39690148..39692016-chr14:39692891..39694587,2 | MCF-7 | breast: | |
| 2 | chr14:39581979..39584975-chr14:39691511..39693486,2 | MCF-7 | breast: | |
| 3 | chr14:39642456..39648509-chr14:39688590..39693921,7 | MCF-7 | breast: | |
| 4 | chr14:39655421..39657718-chr14:39690495..39693068,2 | K562 | blood: | |
| 5 | chr14:39651862..39654641-chr14:39690512..39693459,3 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000259083 | Chromatin interaction |
| ENSG00000100941 | Chromatin interaction |
| ENSG00000092208 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:14)
| rs_ID | r2[population] |
|---|---|
| rs10137623 | 0.94[CHB][hapmap];0.84[AFR][1000 genomes] |
| rs10140832 | 0.82[ASN][1000 genomes] |
| rs1570131 | 0.88[JPT][hapmap] |
| rs17109030 | 0.83[CHB][hapmap];0.83[JPT][hapmap] |
| rs17621388 | 0.83[CHB][hapmap];0.83[JPT][hapmap] |
| rs17692639 | 0.88[CHB][hapmap];0.88[JPT][hapmap] |
| rs2025028 | 0.82[YRI][hapmap] |
| rs2117337 | 0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs34843498 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs35280646 | 0.94[ASN][1000 genomes] |
| rs7143942 | 0.83[CHB][hapmap];0.88[JPT][hapmap] |
| rs7154632 | 0.88[CHB][hapmap];0.88[JPT][hapmap] |
| rs7155164 | 0.88[JPT][hapmap] |
| rs8006182 | 0.83[CHB][hapmap];0.83[JPT][hapmap] |
Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1246 | chr14:39656597-39701520 | Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription | TF binding regionChromatin interactive regionlncRNA | 12 gene(s) | inside rSNPs | diseases |
| 2 | nsv1053133 | chr14:39657535-39770729 | Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 16 gene(s) | inside rSNPs | diseases |
| 3 | nsv977619 | chr14:39690884-39697666 | Enhancers Flanking Active TSS Weak transcription | TF binding regionChromatin interactive region | 7 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:3)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs34664345 | TRAPPC6B | cis | multi-tissue | Pritchard |
| rs34664345 | TRAPPC6B | cis | cerebellum | SCAN |
| rs34664345 | SEC23A | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr14:39674000-39705400 | Weak transcription | H1 BMP4 Derived Mesendoderm Cultured Cells | ES cell derived |
| 2 | chr14:39688800-39693000 | Weak transcription | HepG2 | liver |
