Variant report
| Variant | rs9647353 |
|---|---|
| Chromosome Location | chr3:42713014-42713015 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:7)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:7 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr3:42661746..42664078-chr3:42712950..42714516,2 | K562 | blood: | |
| 2 | chr3:42712017..42714331-chr3:42717093..42719495,2 | K562 | blood: | |
| 3 | chr3:42707503..42709270-chr3:42712561..42714862,2 | MCF-7 | breast: | |
| 4 | chr3:42703465..42708475-chr3:42709684..42714527,5 | MCF-7 | breast: | |
| 5 | chr3:42711098..42713056-chr3:42742898..42745395,2 | MCF-7 | breast: | |
| 6 | chr3:42707323..42709990-chr3:42711723..42713357,2 | K562 | blood: | |
| 7 | chr3:42693708..42695946-chr3:42712144..42715197,4 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000010282 | Chromatin interaction |
| ENSG00000230084 | Chromatin interaction |
| ENSG00000114853 | Chromatin interaction |
| ENSG00000240203 | Chromatin interaction |
| ENSG00000230970 | Chromatin interaction |
| ENSG00000114857 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:11)
| rs_ID | r2[population] |
|---|---|
| rs11129967 | 0.82[TSI][hapmap] |
| rs11712706 | 0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs17074664 | 1.00[YRI][hapmap] |
| rs17074669 | 1.00[YRI][hapmap] |
| rs17074680 | 1.00[YRI][hapmap] |
| rs17238798 | 0.82[ASW][hapmap] |
| rs3821836 | 1.00[YRI][hapmap] |
| rs4371488 | 0.84[ASW][hapmap];0.95[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs4682856 | 0.82[ASW][hapmap] |
| rs62248851 | 0.98[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs6793102 | 0.81[JPT][hapmap];0.84[TSI][hapmap] |
Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1002944 | chr3:42559762-42728909 | Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 41 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:4)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs9647353 | HHATL | cis | parietal | SCAN |
| rs9647353 | FYCO1 | cis | cerebellum | SCAN |
| rs9647353 | EXOSC7 | cis | cerebellum | SCAN |
| rs9647353 | HHATL | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr3:42710000-42715200 | Weak transcription | Fetal Heart | heart |
