Variant report
| Variant | rs16861540 |
|---|---|
| Chromosome Location | chr1:168751899-168751900 |
| allele | A/C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:11)
- CpG islands (count:0)
- Chromatin interactive region (count:6)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:11 , 50 per page) page:
1
| No data |
(count:6 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr1:168750443..168753211-chr1:169074233..169077019,2 | MCF-7 | breast: | |
| 2 | chr1:168745044..168747432-chr1:168750860..168753701,2 | K562 | blood: | |
| 3 | chr1:168750594..168752167-chr1:169074080..169075960,2 | MCF-7 | breast: | |
| 4 | chr1:168745883..168748242-chr1:168750356..168753264,2 | MCF-7 | breast: | |
| 5 | chr1:168742365..168745315-chr1:168750346..168752707,2 | MCF-7 | breast: | |
| 6 | chr1:168742907..168744935-chr1:168749748..168752648,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| LINC00626 | TF binding region |
| ENSG00000143153 | Chromatin interaction |
| ENSG00000235736 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:15)
| rs_ID | r2[population] |
|---|---|
| rs16861543 | 0.82[YRI][hapmap];1.00[AMR][1000 genomes] |
| rs16861544 | 1.00[AMR][1000 genomes] |
| rs16861545 | 1.00[AMR][1000 genomes] |
| rs16861558 | 1.00[AMR][1000 genomes] |
| rs16861563 | 1.00[AMR][1000 genomes] |
| rs2206297 | 1.00[AMR][1000 genomes] |
| rs2206298 | 1.00[AMR][1000 genomes] |
| rs57305392 | 1.00[AMR][1000 genomes] |
| rs73028610 | 1.00[AMR][1000 genomes] |
| rs73036041 | 1.00[AMR][1000 genomes] |
| rs73036057 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs73038220 | 1.00[AMR][1000 genomes] |
| rs73043974 | 1.00[AMR][1000 genomes] |
| rs7515871 | 0.96[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs7516889 | 1.00[AMR][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 | nsv869415 | chr1:168467284-169153863 | Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 44 gene(s) | inside rSNPs | diseases |
| 2 | nsv831847 | chr1:168669877-168850129 | Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 9 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:168751600-168754200 | Enhancers | Hela-S3 | cervix |
