Variant report
| Variant | rs34721465 |
|---|---|
| Chromosome Location | chr3:42714112-42714113 |
| 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 | chr3:42713506..42715721-chr3:42783952..42785579,2 | K562 | blood: | |
| 5 | chr3:42703465..42708475-chr3:42709684..42714527,5 | MCF-7 | breast: | |
| 6 | chr3:42713022..42715006-chr3:42718791..42720637,2 | MCF-7 | breast: | |
| 7 | chr3:42693708..42695946-chr3:42712144..42715197,4 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000114853 | Chromatin interaction |
| ENSG00000230084 | Chromatin interaction |
| ENSG00000114857 | Chromatin interaction |
| ENSG00000240203 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:17)
| rs_ID | r2[population] |
|---|---|
| rs13064597 | 0.91[EUR][1000 genomes] |
| rs13085143 | 0.87[EUR][1000 genomes] |
| rs13086680 | 0.93[AMR][1000 genomes];0.96[EUR][1000 genomes] |
| rs13100261 | 0.90[EUR][1000 genomes] |
| rs2290976 | 0.95[AMR][1000 genomes];0.97[EUR][1000 genomes] |
| rs339705 | 0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs339708 | 0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs34077739 | 0.87[EUR][1000 genomes] |
| rs34196076 | 0.87[EUR][1000 genomes] |
| rs34243788 | 0.90[EUR][1000 genomes] |
| rs35384559 | 0.90[EUR][1000 genomes] |
| rs3733059 | 0.90[AMR][1000 genomes];0.94[EUR][1000 genomes] |
| rs3733061 | 0.95[AMR][1000 genomes];0.96[EUR][1000 genomes] |
| rs55959327 | 0.82[EUR][1000 genomes] |
| rs58645732 | 0.90[EUR][1000 genomes] |
| rs66933062 | 0.96[EUR][1000 genomes] |
| rs67174294 | 0.91[EUR][1000 genomes] |
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:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs34721465 | SEC22C | cis | Muscle Skeletal | GTEx |
| rs34721465 | CCDC13 | cis | Whole Blood | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr3:42710000-42715200 | Weak transcription | Fetal Heart | heart |
