Variant report
| Variant | rs12188638 |
|---|---|
| Chromosome Location | chr5:90539072-90539073 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:6)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:6 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr5:90537317..90540485-chr5:90676988..90679606,3 | K562 | blood: | |
| 2 | chr5:90527291..90547553-chr5:90674171..90681359,33 | K562 | blood: | |
| 3 | chr5:90535308..90537447-chr5:90538676..90541524,2 | MCF-7 | breast: | |
| 4 | chr5:90538867..90541138-chr5:90677587..90679233,2 | MCF-7 | breast: | |
| 5 | chr5:90539006..90540710-chr5:90545437..90546997,2 | K562 | blood: | |
| 6 | chr5:90536554..90539135-chr5:90678170..90680812,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000113369 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:26)
| rs_ID | r2[population] |
|---|---|
| rs10474341 | 1.00[ASN][1000 genomes] |
| rs12514996 | 0.90[ASN][1000 genomes] |
| rs12515116 | 0.93[ASN][1000 genomes] |
| rs12520306 | 1.00[ASN][1000 genomes] |
| rs12653995 | 0.97[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs12658748 | 0.95[ASN][1000 genomes] |
| rs16869618 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs2175437 | 0.87[EUR][1000 genomes] |
| rs56316727 | 0.91[ASN][1000 genomes] |
| rs56377435 | 0.88[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs58781250 | 0.82[ASN][1000 genomes] |
| rs72786311 | 1.00[AFR][1000 genomes];1.00[ASN][1000 genomes] |
| rs72786312 | 0.93[ASN][1000 genomes] |
| rs72786318 | 1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs72786321 | 0.91[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs72786324 | 0.91[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs72786325 | 1.00[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs72786326 | 1.00[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs72786329 | 0.97[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs72786331 | 0.88[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs72786332 | 0.97[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs72786338 | 0.90[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs72786350 | 0.86[ASN][1000 genomes] |
| rs72786353 | 0.82[ASN][1000 genomes] |
| rs72786354 | 0.82[ASN][1000 genomes] |
| rs9647558 | 1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page:
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| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1024813 | chr5:90321535-90870739 | Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 84 gene(s) | inside rSNPs | diseases |
| 2 | nsv537806 | chr5:90321535-90870739 | Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 84 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr5:90525000-90542800 | Weak transcription | Breast variant Human Mammary Epithelial Cells (vHMEC) | Breast |
| 2 | chr5:90530800-90539600 | Weak transcription | Pancreas | Pancrea |
