Variant report
| Variant | rs192172 |
|---|---|
| Chromosome Location | chr5:97965864-97965865 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
| No data |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:24)
| rs_ID | r2[population] |
|---|---|
| rs149508 | 1.00[CHB][hapmap];1.00[ASN][1000 genomes] |
| rs154198 | 0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs160717 | 0.91[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs160721 | 1.00[ASN][1000 genomes] |
| rs160722 | 0.86[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs27020 | 1.00[ASN][1000 genomes] |
| rs27578 | 0.85[AMR][1000 genomes];0.89[EUR][1000 genomes] |
| rs27706 | 1.00[ASN][1000 genomes] |
| rs294029 | 0.85[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs316507 | 0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs379915 | 0.87[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs391352 | 0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs40173 | 1.00[ASN][1000 genomes] |
| rs40807 | 1.00[ASN][1000 genomes] |
| rs439228 | 0.84[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs456509 | 0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs457294 | 0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs457827 | 0.85[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs460980 | 0.85[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs463403 | 0.85[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs466068 | 0.82[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs466154 | 0.84[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs469731 | 1.00[ASN][1000 genomes] |
| rs469946 | 1.00[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1016611 | chr5:97873846-98035559 | Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer | TF binding regionCpG islandChromatin interactive region | 5 gene(s) | inside rSNPs | diseases |
| 2 | nsv537816 | chr5:97873846-98035559 | Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS | TF binding regionCpG islandChromatin interactive region | 5 gene(s) | inside rSNPs | diseases |
| 3 | nsv1029509 | chr5:97888644-98040172 | ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS | TF binding regionCpG islandChromatin interactive region | 3 gene(s) | inside rSNPs | diseases |
| 4 | nsv882413 | chr5:97918829-98022320 | Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer | TF binding regionCpG islandChromatin interactive region | 2 gene(s) | inside rSNPs | diseases |
| 5 | esv1832089 | chr5:97934125-97976039 | Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats | TF binding regionCpG islandChromatin interactive region | 1 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:3)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs192172 | RGMB | Cis_1M | lymphoblastoid | RTeQTL |
| rs192172 | SLCO4C1 | cis | parietal | SCAN |
| rs192172 | RGMB | cis | lymphoblastoid | seeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr5:97946400-97967200 | Weak transcription | HSMMtube | muscle |
| 2 | chr5:97965800-97968400 | Weak transcription | hESC Derived CD184+ Endoderm Cultured Cells | ES cell derived |
