Variant report
| Variant | rs16833852 |
|---|---|
| Chromosome Location | chr1:152098716-152098717 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:2)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:2 , 50 per page) page:
1
| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | GATA3 | chr1:152098364-152099036 | MCF-7 | breast: | n/a | chr1:152098738-152098755 chr1:152098740-152098747 chr1:152098733-152098749 chr1:152098735-152098747 |
| 2 | GATA3 | chr1:152098207-152099096 | MCF-7 | breast: | n/a | chr1:152098738-152098755 chr1:152098740-152098747 chr1:152098733-152098749 chr1:152098735-152098747 |
| No data |
(count:1 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr1:152092225..152095424-chr1:152096405..152099534,4 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| HDHD1P2 | TF binding region |
| ENSG00000226716 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:13)
| rs_ID | r2[population] |
|---|---|
| rs11204924 | 1.00[YRI][hapmap];0.96[AFR][1000 genomes] |
| rs12086674 | 0.88[AFR][1000 genomes] |
| rs12091228 | 1.00[YRI][hapmap];0.83[AFR][1000 genomes] |
| rs3922963 | 0.92[AFR][1000 genomes] |
| rs4631697 | 0.92[AFR][1000 genomes] |
| rs4634912 | 1.00[LWK][hapmap];0.91[MKK][hapmap];0.92[AFR][1000 genomes] |
| rs6658550 | 0.88[AFR][1000 genomes] |
| rs6673322 | 0.88[AFR][1000 genomes] |
| rs6694472 | 1.00[YRI][hapmap];0.92[AFR][1000 genomes] |
| rs7539086 | 1.00[YRI][hapmap];1.00[AFR][1000 genomes] |
| rs7540075 | 0.85[AFR][1000 genomes] |
| rs7540580 | 0.96[AFR][1000 genomes] |
| rs7554343 | 1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap] |
Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1007097 | chr1:151832796-152227977 | Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 196 gene(s) | inside rSNPs | diseases |
| 2 | nsv1012327 | chr1:151835544-152200890 | Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 196 gene(s) | inside rSNPs | diseases |
| 3 | nsv535159 | chr1:151835544-152200890 | Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 196 gene(s) | inside rSNPs | diseases |
| 4 | nsv547853 | chr1:152008671-152236760 | Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 83 gene(s) | inside rSNPs | diseases |
| 5 | nsv872442 | chr1:152054120-152187641 | Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 9 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:152098000-152099000 | Enhancers | Fetal Thymus | thymus |
| 2 | chr1:152098200-152098800 | Enhancers | Thymus | Thymus |
