Variant report
| Variant | rs17257039 |
|---|---|
| Chromosome Location | chr4:119603703-119603704 |
| allele | A/G |
| 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:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr4:119603589..119605828-chr4:119610331..119611922,3 | MCF-7 | breast: | |
| 2 | chr4:119598821..119601848-chr4:119602185..119606095,4 | K562 | blood: | |
| 3 | chr4:119602965..119604556-chr4:119604808..119606463,2 | K562 | blood: | |
| 4 | chr4:119199307..119202288-chr4:119603050..119607934,6 | MCF-7 | breast: | |
| 5 | chr4:119603174..119605394-chr4:120137644..120139212,2 | K562 | blood: | |
| 6 | chr4:119508532..119510926-chr4:119602289..119604089,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000269893 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:19)
| rs_ID | r2[population] |
|---|---|
| rs11098451 | 0.92[CEU][hapmap] |
| rs11931194 | 0.91[AMR][1000 genomes] |
| rs11938970 | 0.92[CEU][hapmap];0.91[AMR][1000 genomes] |
| rs17257945 | 0.92[CEU][hapmap];1.00[AFR][1000 genomes] |
| rs17258050 | 1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes] |
| rs17258106 | 0.92[CEU][hapmap];1.00[AFR][1000 genomes] |
| rs17258830 | 0.83[CEU][hapmap] |
| rs17258907 | 0.89[CEU][hapmap] |
| rs17323012 | 0.92[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes] |
| rs17323034 | 0.83[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes] |
| rs17323877 | 1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes] |
| rs17324884 | 0.83[CEU][hapmap] |
| rs17324968 | 0.83[CEU][hapmap] |
| rs28627331 | 1.00[AFR][1000 genomes] |
| rs41455648 | 0.92[CEU][hapmap] |
| rs55634130 | 1.00[AFR][1000 genomes];0.91[AMR][1000 genomes] |
| rs56000725 | 1.00[AFR][1000 genomes];0.91[AMR][1000 genomes] |
| rs56225646 | 1.00[AFR][1000 genomes];0.91[AMR][1000 genomes] |
| rs73842212 | 0.91[AMR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:3 , 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 | nsv519017 | chr4:118828807-119771481 | Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 39 gene(s) | inside rSNPs | diseases |
| 2 | esv3355840 | chr4:119296640-119774737 | Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 20 gene(s) | inside rSNPs | diseases |
| 3 | nsv427693 | chr4:119493919-119674742 | Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 16 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr4:119592800-119606200 | Weak transcription | Breast Myoepithelial Primary Cells | Breast |
| 2 | chr4:119603600-119603800 | Enhancers | Breast variant Human Mammary Epithelial Cells (vHMEC) | Breast |
