Variant report
| Variant | rs1547725 |
|---|---|
| Chromosome Location | chr1:165670958-165670959 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:2)
- 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 | chr1:165665438..165667990-chr1:165670115..165672105,2 | K562 | blood: |
(count:2 , 50 per page) page:
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| No. | lncRNA name | Chromosome Location | lncRNA alias |
|---|---|---|---|
| 1 | lnc-MGST3-2 | chr1:165670918-165671228 | ENSG00000215838.3 |
| 2 | lnc-MGST3-2 | chr1:165670918-165671228 | NR_036683 |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000215838 | Chromatin interaction |
| ENSG00000143149 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:27)
| rs_ID | r2[population] |
|---|---|
| rs10800135 | 1.00[JPT][hapmap];1.00[ASN][1000 genomes] |
| rs10800153 | 0.82[AMR][1000 genomes] |
| rs10800154 | 0.80[AMR][1000 genomes] |
| rs10800155 | 1.00[JPT][hapmap] |
| rs12133745 | 0.82[AMR][1000 genomes] |
| rs12403369 | 1.00[JPT][hapmap] |
| rs2251768 | 0.91[CEU][hapmap];1.00[JPT][hapmap] |
| rs2790052 | 0.91[CEU][hapmap];1.00[JPT][hapmap] |
| rs2790053 | 0.91[CEU][hapmap];1.00[JPT][hapmap] |
| rs2814466 | 1.00[JPT][hapmap] |
| rs2814471 | 0.91[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap] |
| rs4537525 | 1.00[JPT][hapmap];0.82[AMR][1000 genomes] |
| rs4603103 | 0.82[AMR][1000 genomes] |
| rs4656460 | 1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs4656461 | 0.91[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.80[AMR][1000 genomes] |
| rs4657471 | 1.00[JPT][hapmap];0.86[AMR][1000 genomes] |
| rs4657474 | 0.80[AMR][1000 genomes] |
| rs4657475 | 0.80[AMR][1000 genomes] |
| rs4657476 | 0.91[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap] |
| rs4657477 | 0.91[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap] |
| rs6426936 | 0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs6660601 | 0.91[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes] |
| rs6668108 | 0.80[AMR][1000 genomes] |
| rs6696454 | 0.91[CEU][hapmap];0.82[AMR][1000 genomes] |
| rs7518099 | 0.91[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap] |
| rs7524755 | 0.91[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes] |
| rs7555523 | 0.91[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap] |
Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | esv2756102 | chr1:165652342-165877342 | Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 48 gene(s) | inside rSNPs | diseases |
| 2 | nsv1011720 | chr1:165669589-165802516 | Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 41 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:165668200-165671000 | Weak transcription | Liver | Liver |
| 2 | chr1:165670200-165673200 | Enhancers | HepG2 | liver |
