Variant report
| Variant | rs1738334 |
|---|---|
| Chromosome Location | chr6:49316238-49316239 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:1 , 50 per page) page:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr6:49305110..49306958-chr6:49313683..49316674,2 | K562 | blood: |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:7)
| rs_ID | r2[population] |
|---|---|
| rs493700 | 0.87[AFR][1000 genomes] |
| rs504213 | 0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs540785 | 0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs556046 | 0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs562112 | 0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs570475 | 0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs571140 | 0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[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 | nsv1024959 | chr6:49290141-49652124 | Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 19 gene(s) | inside rSNPs | diseases |
| 2 | nsv1021136 | chr6:49295037-49631278 | Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 19 gene(s) | inside rSNPs | diseases |
| 3 | nsv915806 | chr6:49313295-49430422 | Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionmiRNA target site | 7 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:10)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs1738334 | MUT | cis | Artery Tibial | GTEx |
| rs1738334 | CENPQ | cis | Artery Tibial | GTEx |
| rs1738334 | CENPQ | cis | Adipose Subcutaneous | GTEx |
| rs1738334 | CENPQ | Cis_1M | lymphoblastoid | RTeQTL |
| rs1738334 | CENPQ | cis | Esophagus Muscularis | GTEx |
| rs1738334 | CENPQ | cis | Nerve Tibial | GTEx |
| rs1738334 | MUT | Cis_1M | lymphoblastoid | RTeQTL |
| rs1738334 | MUT | cis | Nerve Tibial | GTEx |
| rs1738334 | CENPQ | cis | Thyroid | GTEx |
| rs1738334 | CENPQ | cis | lung | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr6:49310800-49328000 | Weak transcription | Breast variant Human Mammary Epithelial Cells (vHMEC) | Breast |
