Variant report
| Variant | rs2968825 |
|---|---|
| Chromosome Location | chr2:55303042-55303043 |
| allele | G/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 | chr2:55276298..55277935-chr2:55301112..55303526,2 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000115310 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:16)
| rs_ID | r2[population] |
|---|---|
| rs11674808 | 0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs13011689 | 0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs2920862 | 0.94[ASN][1000 genomes] |
| rs2920878 | 0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs2920900 | 0.86[EUR][1000 genomes];0.83[ASN][1000 genomes] |
| rs2968790 | 0.86[EUR][1000 genomes];0.85[ASN][1000 genomes] |
| rs2968793 | 0.87[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs2968794 | 0.89[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs2968795 | 0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs2968798 | 0.94[ASN][1000 genomes] |
| rs2968822 | 0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs2968827 | 0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs2972070 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs2972071 | 0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs2972072 | 0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs2972075 | 0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:1 , 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 | nsv874155 | chr2:55205262-55307646 | Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 37 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:7)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs2968825 | RTN4 | cis | Thyroid | GTEx |
| rs2968825 | RTN4 | cis | Skin Sun Exposed Lower leg | GTEx |
| rs2968825 | RTN4 | cis | Artery Tibial | GTEx |
| rs2968825 | RTN4 | cis | Whole Blood | GTEx |
| rs2968825 | RTN4 | cis | Nerve Tibial | GTEx |
| rs2968825 | RTN4 | cis | Artery Aorta | GTEx |
| rs2968825 | RTN4 | cis | Esophagus Mucosa | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr2:55299200-55318000 | Weak transcription | H1 Derived Mesenchymal Stem Cells | ES cell derived |
| 2 | chr2:55303000-55304200 | Enhancers | HUVEC | blood vessel |
