Variant report
| Variant | rs58499470 |
|---|---|
| Chromosome Location | chr19:40192400-40192401 |
| allele | A/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:13)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:13 , 50 per page) page:
1
| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | STAT3 | chr19:40191984-40192434 | GM12878 | blood: | n/a | n/a |
| 2 | MTA3 | chr19:40191628-40192524 | GM12878 | blood: | n/a | n/a |
| 3 | RCOR1 | chr19:40191835-40192609 | GM12878 | blood: | n/a | n/a |
| 4 | RUNX3 | chr19:40191796-40192423 | GM12878 | blood: | n/a | n/a |
| 5 | MEF2A | chr19:40191900-40192452 | GM12878 | blood: | n/a | n/a |
| 6 | FOXM1 | chr19:40191822-40192432 | GM12878 | blood: | n/a | n/a |
| 7 | ATF2 | chr19:40191735-40192471 | GM12878 | blood: | n/a | n/a |
| 8 | EBF1 | chr19:40191971-40192404 | GM12878 | blood: | n/a | n/a |
| 9 | NFIC | chr19:40191841-40192497 | GM12878 | blood: | n/a | n/a |
| 10 | EP300 | chr19:40191912-40192431 | GM12878 | blood: | n/a | n/a |
| 11 | BHLHE40 | chr19:40191938-40192401 | GM12878 | blood: | n/a | n/a |
| 12 | FOXM1 | chr19:40191745-40192501 | GM12878 | blood: | n/a | n/a |
| 13 | TBP | chr19:40191864-40192448 | GM12878 | blood: | n/a | n/a |
| No data |
(count:1 , 50 per page) page:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr19:40191402..40192980-chr19:40193546..40196170,2 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| LGALS14 | TF binding region |
| ENSG00000006659 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:12)
| rs_ID | r2[population] |
|---|---|
| rs58551684 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs59313124 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs73543013 | 1.00[AMR][1000 genomes] |
| rs73557828 | 0.89[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs73557836 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs73557840 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs73557870 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs73557875 | 1.00[AFR][1000 genomes] |
| rs73557877 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs73557895 | 1.00[AMR][1000 genomes] |
| rs73559703 | 1.00[AMR][1000 genomes] |
| rs73559744 | 1.00[AMR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1057361 | chr19:40123868-40310996 | Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 19 gene(s) | inside rSNPs | diseases |
| 2 | nsv1061361 | chr19:40131820-40310996 | Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 17 gene(s) | inside rSNPs | diseases |
| 3 | nsv579511 | chr19:40132825-40310497 | Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 17 gene(s) | inside rSNPs | diseases |
| 4 | nsv1062394 | chr19:40133229-40310186 | Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 17 gene(s) | inside rSNPs | diseases |
| 5 | nsv544004 | chr19:40133229-40310186 | Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 17 gene(s) | inside rSNPs | diseases |
| 6 | esv3397881 | chr19:40150495-40199437 | Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 11 gene(s) | inside rSNPs | diseases |
| 7 | nsv1059691 | chr19:40168862-40306373 | Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 12 gene(s) | inside rSNPs | diseases |
| 8 | nsv544005 | chr19:40168862-40306373 | Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 12 gene(s) | inside rSNPs | diseases |
| 9 | esv3332670 | chr19:40181720-40297955 | Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 8 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr19:40188400-40192800 | Weak transcription | Placenta | Placenta |
| 2 | chr19:40191600-40192800 | Flanking Active TSS | GM12878-XiMat | blood |
| 3 | chr19:40192400-40193200 | Weak transcription | iPS DF 19.11 Cell Line | embryonic stem cell |
