Variant report
| Variant | rs9342044 |
|---|---|
| Chromosome Location | chr6:86414030-86414031 |
| 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:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr6:86385142..86387483-chr6:86411615..86414165,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000203875 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:13)
| rs_ID | r2[population] |
|---|---|
| rs1173417 | 0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs2475787 | 1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs2475792 | 0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes] |
| rs4383777 | 0.89[ASN][1000 genomes] |
| rs6454486 | 0.86[ASN][1000 genomes] |
| rs7752502 | 0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs7762321 | 0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs9342046 | 0.89[ASN][1000 genomes] |
| rs9344542 | 0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes] |
| rs9353327 | 0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes] |
| rs9362239 | 0.86[ASN][1000 genomes] |
| rs9450318 | 0.89[ASN][1000 genomes] |
| rs9450319 | 0.88[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1028293 | chr6:86353958-86778912 | Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 100 gene(s) | inside rSNPs | diseases |
| 2 | nsv538350 | chr6:86353958-86778912 | Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 100 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:13)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs9342044 | SNHG5 | cis | Adipose Subcutaneous | GTEx |
| rs9342044 | SNHG5 | cis | Thyroid | GTEx |
| rs9342044 | SNHG5 | cis | Skin Sun Exposed Lower leg | GTEx |
| rs9342044 | SNHG5 | cis | Nerve Tibial | GTEx |
| rs9342044 | SNHG5 | cis | Esophagus Muscularis | GTEx |
| rs9342044 | SNHG5 | cis | Whole Blood | GTEx |
| rs9342044 | SNHG5 | cis | Heart Left Ventricle | GTEx |
| rs9342044 | SNHG5 | cis | lung | GTEx |
| rs9342044 | SNHG5 | cis | Artery Tibial | GTEx |
| rs9342044 | SNHG5 | cis | Esophagus Mucosa | GTEx |
| rs9342044 | SNHG5 | Cis_1M | lymphoblastoid | RTeQTL |
| rs9342044 | SNHG5 | cis | Muscle Skeletal | GTEx |
| rs9342044 | SNHG5 | cis | Artery Aorta | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr6:86410600-86414800 | Weak transcription | iPS DF 19.11 Cell Line | embryonic stem cell |
