Variant report
| Variant | rs4502159 |
|---|---|
| Chromosome Location | chr15:50468959-50468960 |
| allele | A/C |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:4)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:4 , 50 per page) page:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr15:50467982..50471005-chr15:50472015..50474960,3 | K562 | blood: | |
| 2 | chr15:50467355..50470733-chr15:50646637..50649542,3 | MCF-7 | breast: | |
| 3 | chr15:50468307..50471264-chr15:50485331..50487376,2 | MCF-7 | breast: | |
| 4 | chr15:50467355..50471725-chr15:50472590..50476419,7 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000244879 | Chromatin interaction |
| ENSG00000104064 | Chromatin interaction |
| ENSG00000104043 | Chromatin interaction |
| ENSG00000140284 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:4)
| rs_ID | r2[population] |
|---|---|
| rs11637647 | 1.00[ASN][1000 genomes] |
| rs12438280 | 0.84[JPT][hapmap] |
| rs2853766 | 1.00[LWK][hapmap] |
| rs6493393 | 0.84[ASW][hapmap] |
Variant overlapped rSNPs/rCNVs (count:7 , 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 | nsv1044277 | chr15:49921547-50702386 | Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 107 gene(s) | inside rSNPs | diseases |
| 2 | nsv542380 | chr15:49921547-50702386 | Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 107 gene(s) | inside rSNPs | diseases |
| 3 | nsv1035983 | chr15:50223334-50595170 | Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 15 gene(s) | inside rSNPs | diseases |
| 4 | nsv542382 | chr15:50223334-50595170 | Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 15 gene(s) | inside rSNPs | diseases |
| 5 | nsv904209 | chr15:50444824-50482133 | Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats | TF binding regionCpG islandChromatin interactive region | 5 gene(s) | inside rSNPs | diseases |
| 6 | nsv525505 | chr15:50468959-50469288 | Enhancers Weak transcription | Chromatin interactive region | 4 gene(s) | inside rSNPs | diseases |
| 7 | nsv526926 | chr15:50468959-50469288 | Enhancers Weak transcription | Chromatin interactive region | 4 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:4)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs4502159 | ATP8B4 | cis | cerebellum | SCAN |
| rs4502159 | SLC27A2 | cis | cerebellum | SCAN |
| rs4502159 | MYO1E | trans | cerebellum | SCAN |
| rs4502159 | FRMD5 | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr15:50461600-50472400 | Weak transcription | Hela-S3 | cervix |
| 2 | chr15:50468800-50469000 | Enhancers | Foreskin Keratinocyte Primary Cells skin02 | Skin |
