Variant report
| Variant | rs2140078 |
|---|---|
| Chromosome Location | chr3:179798401-179798402 |
| 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:29)
| rs_ID | r2[population] |
|---|---|
| rs10513768 | 0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs10937018 | 0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs13066273 | 0.92[ASN][1000 genomes] |
| rs1402965 | 0.99[ASN][1000 genomes] |
| rs1522118 | 0.91[ASN][1000 genomes] |
| rs1522122 | 0.88[ASN][1000 genomes] |
| rs1608071 | 0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs1608073 | 0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs1608074 | 0.99[ASN][1000 genomes] |
| rs1608075 | 0.99[ASN][1000 genomes] |
| rs1915906 | 0.94[ASN][1000 genomes] |
| rs1915908 | 0.84[ASN][1000 genomes] |
| rs2177130 | 0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs34582044 | 0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs4376038 | 0.82[ASN][1000 genomes] |
| rs4501114 | 0.99[ASN][1000 genomes] |
| rs4855139 | 0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs4855140 | 0.90[ASN][1000 genomes] |
| rs6771471 | 0.99[ASN][1000 genomes] |
| rs6786266 | 0.99[ASN][1000 genomes] |
| rs6806300 | 0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs7618051 | 0.82[ASN][1000 genomes] |
| rs7652876 | 0.84[ASN][1000 genomes] |
| rs950198 | 0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs9809186 | 0.99[ASN][1000 genomes] |
| rs9833099 | 0.92[ASN][1000 genomes] |
| rs9840949 | 0.99[ASN][1000 genomes] |
| rs9850524 | 0.89[ASN][1000 genomes] |
| rs9863729 | 0.92[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv534210 | chr3:179666123-179899347 | Enhancers Bivalent Enhancer Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
| 2 | nsv1000756 | chr3:179672703-179827373 | Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 1 gene(s) | inside rSNPs | diseases |
| 3 | nsv1012880 | chr3:179772283-179835563 | Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS | Chromatin interactive region | n/a | inside rSNPs | diseases |
| 4 | esv275254 | chr3:179786726-179802042 | Enhancers Weak transcription | n/a | n/a | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs2140078 | ZMAT3 | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr3:179792400-179809800 | Weak transcription | Breast variant Human Mammary Epithelial Cells (vHMEC) | Breast |
