Variant report
| Variant | rs2124228 |
|---|---|
| Chromosome Location | chr18:11339759-11339760 |
| 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 | chr18:11324796..11327150-chr18:11338669..11340267,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000263682 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:37)
| rs_ID | r2[population] |
|---|---|
| rs1455246 | 1.00[ASN][1000 genomes] |
| rs16976151 | 0.97[ASN][1000 genomes] |
| rs16976152 | 0.97[ASN][1000 genomes] |
| rs16976153 | 0.97[ASN][1000 genomes] |
| rs1874772 | 1.00[ASN][1000 genomes] |
| rs28380540 | 1.00[ASN][1000 genomes] |
| rs28406157 | 1.00[ASN][1000 genomes] |
| rs28496831 | 1.00[ASN][1000 genomes] |
| rs28505571 | 0.97[ASN][1000 genomes] |
| rs28713321 | 1.00[ASN][1000 genomes] |
| rs28762125 | 1.00[ASN][1000 genomes] |
| rs36057401 | 1.00[ASN][1000 genomes] |
| rs59591408 | 1.00[ASN][1000 genomes] |
| rs7230024 | 1.00[ASN][1000 genomes] |
| rs7231185 | 0.97[ASN][1000 genomes] |
| rs73402984 | 0.97[ASN][1000 genomes] |
| rs73402985 | 0.97[ASN][1000 genomes] |
| rs8092521 | 1.00[ASN][1000 genomes] |
| rs8092523 | 1.00[ASN][1000 genomes] |
| rs8094486 | 1.00[ASN][1000 genomes] |
| rs8094727 | 1.00[ASN][1000 genomes] |
| rs8095281 | 1.00[ASN][1000 genomes] |
| rs902969 | 1.00[ASN][1000 genomes] |
| rs902970 | 1.00[ASN][1000 genomes] |
| rs9950278 | 1.00[ASN][1000 genomes] |
| rs9950284 | 0.94[ASN][1000 genomes] |
| rs9951023 | 1.00[JPT][hapmap];0.97[ASN][1000 genomes] |
| rs9953018 | 1.00[ASN][1000 genomes] |
| rs9955801 | 1.00[ASN][1000 genomes] |
| rs9956107 | 1.00[ASN][1000 genomes] |
| rs9956498 | 1.00[ASN][1000 genomes] |
| rs9959689 | 1.00[ASN][1000 genomes] |
| rs9963723 | 1.00[ASN][1000 genomes] |
| rs9964195 | 1.00[ASN][1000 genomes] |
| rs9964199 | 1.00[ASN][1000 genomes] |
| rs9964337 | 1.00[ASN][1000 genomes] |
| rs9965049 | 0.97[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv458029 | chr18:10814334-11662151 | Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA | 26 gene(s) | inside rSNPs | diseases |
| 2 | nsv576480 | chr18:10814334-11662151 | Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA | 26 gene(s) | inside rSNPs | diseases |
| 3 | nsv1066659 | chr18:11246502-11709409 | Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA | 24 gene(s) | inside rSNPs | diseases |
| 4 | nsv1057976 | chr18:11251898-11664914 | Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA | 24 gene(s) | inside rSNPs | diseases |
| 5 | nsv543650 | chr18:11251898-11664914 | Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA | 24 gene(s) | inside rSNPs | diseases |
| 6 | nsv833589 | chr18:11293101-11454521 | Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers | TF binding regionChromatin interactive regionlncRNA | 6 gene(s) | inside rSNPs | diseases |
| 7 | esv3336425 | chr18:11328001-11375388 | Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats | Chromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | n/a |
| 8 | nsv1056541 | chr18:11336695-11558542 | Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 16 gene(s) | inside rSNPs | diseases |
| 9 | nsv543651 | chr18:11336695-11558542 | Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 16 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs2124228 | CA12 | trans | brain | seeQTL |
| rs2124228 | PLIN1 | trans | brain | seeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr18:11339400-11349000 | Weak transcription | NHDF-Ad | bronchial |
