Variant report
| Variant | rs331917 |
|---|---|
| Chromosome Location | chr5:98158524-98158525 |
| allele | A/G |
| 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 | chr5:98103103..98105635-chr5:98157810..98160192,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000174136 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:7)
| rs_ID | r2[population] |
|---|---|
| rs109843 | 0.88[CEU][hapmap];0.81[JPT][hapmap] |
| rs161937 | 0.96[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap] |
| rs326488 | 0.86[AMR][1000 genomes];0.85[EUR][1000 genomes] |
| rs327786 | 0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes] |
| rs331547 | 0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs34487 | 0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes] |
| rs692759 | 0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv882414 | chr5:98063710-98193164 | Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 11 gene(s) | inside rSNPs | diseases |
| 2 | nsv882415 | chr5:98134186-98312447 | Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 36 gene(s) | inside rSNPs | diseases |
| 3 | nsv882416 | chr5:98146106-98312447 | Bivalent/Poised TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 35 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs331917 | RGMB | Cis_1M | lymphoblastoid | RTeQTL |
Chromatin state (count:0 , 50 per page) page:
| No data |
