Variant report
| Variant | rs12459746 |
|---|---|
| Chromosome Location | chr19:38857085-38857086 |
| allele | C/T |
| 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:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr19:38855795..38857847-chr19:38858914..38861126,2 | MCF-7 | breast: | |
| 2 | chr19:38856161..38860758-chr19:38862058..38866841,9 | MCF-7 | breast: | |
| 3 | chr19:38852371..38854789-chr19:38855847..38858452,2 | MCF-7 | breast: | |
| 4 | chr19:38847354..38850144-chr19:38856226..38859199,2 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000099341 | Chromatin interaction |
| ENSG00000266963 | Chromatin interaction |
| ENSG00000099338 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:12)
| rs_ID | r2[population] |
|---|---|
| rs11666449 | 0.94[CHB][hapmap];0.85[CHD][hapmap];0.80[ASN][1000 genomes] |
| rs11671779 | 0.89[CEU][hapmap] |
| rs11673012 | 0.89[CEU][hapmap] |
| rs11673222 | 0.89[CEU][hapmap];0.85[TSI][hapmap] |
| rs2270093 | 0.80[EUR][1000 genomes] |
| rs2270094 | 0.89[CEU][hapmap];0.83[CHB][hapmap];0.85[CHD][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes] |
| rs3745951 | 0.89[CEU][hapmap];0.85[TSI][hapmap] |
| rs4386247 | 0.89[CEU][hapmap];0.85[TSI][hapmap] |
| rs4804046 | 0.89[CEU][hapmap];0.85[TSI][hapmap] |
| rs8106900 | 0.88[CEU][hapmap];0.85[TSI][hapmap] |
| rs931749 | 0.89[CEU][hapmap];0.85[TSI][hapmap] |
| rs931750 | 0.89[CEU][hapmap];0.82[TSI][hapmap] |
Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1063471 | chr19:38734744-39148392 | Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 73 gene(s) | inside rSNPs | diseases |
| 2 | nsv833822 | chr19:38760748-38945105 | Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 50 gene(s) | inside rSNPs | diseases |
| 3 | nsv911658 | chr19:38785318-39002140 | Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 55 gene(s) | inside rSNPs | diseases |
| 4 | nsv470140 | chr19:38840139-39119494 | Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 43 gene(s) | inside rSNPs | diseases |
| 5 | nsv911659 | chr19:38852357-39002140 | Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 36 gene(s) | inside rSNPs | diseases |
| 6 | nsv911660 | chr19:38852357-39060238 | Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 41 gene(s) | inside rSNPs | diseases |
| 7 | nsv833823 | chr19:38855550-39035800 | Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 39 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs12459746 | C19orf33 | cis | normal skin | skin_eQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr19:38853800-38864400 | Weak transcription | A549 | lung |
| 2 | chr19:38857000-38857200 | Bivalent Enhancer | ES-UCSF4 Cell Line | embryonic stem cell |
| 3 | chr19:38857000-38857600 | Enhancers | HepG2 | liver |
