Variant report
| Variant | rs4855838 |
|---|---|
| Chromosome Location | chr3:49579876-49579877 |
| 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 | chr3:49577802..49580389-chr3:49589871..49592100,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000226913 | Chromatin interaction |
| ENSG00000164061 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:14)
| rs_ID | r2[population] |
|---|---|
| rs10865956 | 0.87[AFR][1000 genomes] |
| rs11130204 | 0.85[AFR][1000 genomes] |
| rs11130208 | 0.81[AFR][1000 genomes] |
| rs12583 | 0.87[AFR][1000 genomes] |
| rs13322887 | 0.83[AFR][1000 genomes] |
| rs1532204 | 0.81[AFR][1000 genomes] |
| rs1982861 | 0.87[AFR][1000 genomes] |
| rs2312462 | 0.84[AFR][1000 genomes] |
| rs4052546 | 0.84[AFR][1000 genomes] |
| rs4241407 | 0.84[AFR][1000 genomes] |
| rs4855837 | 0.84[AFR][1000 genomes] |
| rs4855853 | 0.80[AFR][1000 genomes] |
| rs6797299 | 0.81[AFR][1000 genomes] |
| rs9871024 | 0.83[AFR][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 | nsv834687 | chr3:49448632-49631788 | Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 56 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:15)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs4855838 | NICN1 | cis | Thyroid | GTEx |
| rs4855838 | WDR6 | cis | Nerve Tibial | GTEx |
| rs4855838 | AMT | cis | Artery Tibial | GTEx |
| rs4855838 | NICN1-AS1 | cis | Thyroid | GTEx |
| rs4855838 | AMT | cis | Artery Aorta | GTEx |
| rs4855838 | AMT | cis | Esophagus Mucosa | GTEx |
| rs4855838 | AMT | cis | Muscle Skeletal | GTEx |
| rs4855838 | WDR6 | cis | Muscle Skeletal | GTEx |
| rs4855838 | WDR6 | cis | Esophagus Muscularis | GTEx |
| rs4855838 | AMT | Cis_1M | lymphoblastoid | RTeQTL |
| rs4855838 | AMT | cis | lung | GTEx |
| rs4855838 | AMT | cis | Whole Blood | GTEx |
| rs4855838 | AMT | cis | Thyroid | GTEx |
| rs4855838 | AMT | cis | Nerve Tibial | GTEx |
| rs4855838 | AMT | cis | Adipose Subcutaneous | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr3:49578200-49581600 | Weak transcription | iPS DF 19.11 Cell Line | embryonic stem cell |
