Variant report
| Variant | rs109843 |
|---|---|
| Chromosome Location | chr5:98320937-98320938 |
| allele | A/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:5)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:5 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr5:98263523..98265530-chr5:98319881..98323105,3 | K562 | blood: | |
| 2 | chr5:98263262..98265632-chr5:98320644..98322475,2 | MCF-7 | breast: | |
| 3 | chr5:98261777..98266971-chr5:98317922..98324645,8 | K562 | blood: | |
| 4 | chr5:98319399..98322324-chr5:98333991..98335687,2 | K562 | blood: | |
| 5 | chr5:98320467..98322089-chr5:98322877..98325395,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000153922 | Chromatin interaction |
| ENSG00000248489 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:8)
| rs_ID | r2[population] |
|---|---|
| rs10070926 | 0.83[AMR][1000 genomes];0.89[EUR][1000 genomes] |
| rs13185489 | 0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs161937 | 0.96[CEU][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes] |
| rs161949 | 0.82[EUR][1000 genomes] |
| rs327786 | 0.92[CEU][hapmap];0.84[JPT][hapmap] |
| rs331917 | 0.88[CEU][hapmap];0.81[JPT][hapmap] |
| rs34487 | 0.92[CEU][hapmap];0.85[JPT][hapmap] |
| rs692759 | 0.96[CEU][hapmap];0.90[JPT][hapmap] |
Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | esv1826071 | chr5:98312447-98358852 | Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats | Chromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | diseases |
| 2 | esv1827754 | chr5:98312447-98358852 | Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS | Chromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | diseases |
| 3 | esv1837772 | chr5:98312447-98358852 | Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats | Chromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | diseases |
| 4 | esv1838335 | chr5:98312447-98358852 | Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats | Chromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | diseases |
| 5 | esv1845131 | chr5:98312447-98358852 | Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats | Chromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | diseases |
| 6 | nsv4930 | chr5:98318768-98350644 | Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS | Chromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs109843 | RGMB | Cis_1M | lymphoblastoid | RTeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr5:98319000-98321400 | Weak transcription | K562 | blood |
