Variant report
| Variant | rs11229362 |
|---|---|
| Chromosome Location | chr11:58090614-58090615 |
| allele | C/T |
| 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:25)
| rs_ID | r2[population] |
|---|---|
| rs10896734 | 0.84[CHB][hapmap];0.92[CHD][hapmap];0.91[JPT][hapmap] |
| rs11229350 | 1.00[ASN][1000 genomes] |
| rs11229358 | 0.94[ASN][1000 genomes] |
| rs11229359 | 0.94[ASN][1000 genomes] |
| rs11229369 | 0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs11229371 | 0.94[ASN][1000 genomes] |
| rs11229438 | 0.84[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap] |
| rs11229440 | 0.84[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap] |
| rs11494130 | 0.96[ASN][1000 genomes] |
| rs11494131 | 0.96[ASN][1000 genomes] |
| rs12361789 | 0.96[ASN][1000 genomes] |
| rs12362065 | 0.84[CHB][hapmap];0.92[CHD][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes] |
| rs12363504 | 0.86[ASN][1000 genomes] |
| rs12364387 | 0.85[ASN][1000 genomes] |
| rs12365107 | 0.83[JPT][hapmap] |
| rs2096558 | 0.83[JPT][hapmap] |
| rs4127347 | 0.86[ASN][1000 genomes] |
| rs4482047 | 0.97[ASN][1000 genomes] |
| rs57106977 | 0.91[ASN][1000 genomes] |
| rs57922517 | 0.99[ASN][1000 genomes] |
| rs58085299 | 0.96[ASN][1000 genomes] |
| rs7111679 | 0.83[JPT][hapmap] |
| rs734777 | 0.93[ASN][1000 genomes] |
| rs73481989 | 0.96[ASN][1000 genomes] |
| rs73484144 | 0.93[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 | nsv1054205 | chr11:57544264-58358509 | Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 67 gene(s) | inside rSNPs | diseases |
| 2 | nsv1039453 | chr11:57924680-58119650 | Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 11 gene(s) | inside rSNPs | diseases |
| 3 | nsv541051 | chr11:57924680-58119650 | Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 11 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs11229362 | MS4A6A | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr11:58084200-58102400 | Weak transcription | Breast variant Human Mammary Epithelial Cells (vHMEC) | Breast |
