Variant report
| Variant | rs28359953 |
|---|---|
| Chromosome Location | chr6:29344179-29344180 |
| allele | G/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:9)
- CpG islands (count:0)
- Chromatin interactive region (count:3)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:9 , 50 per page) page:
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| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | RAD21 | chr6:29343857-29344197 | ECC-1 | luminal epithelium: | n/a | chr6:29343951-29343970 |
| 2 | RAD21 | chr6:29343858-29344286 | SK-N-SH | brain: | n/a | chr6:29343951-29343970 |
| 3 | RAD21 | chr6:29343713-29344272 | HCT-116 | colon: | n/a | chr6:29343951-29343970 |
| 4 | CTCF | chr6:29343664-29344257 | SK-N-SH | brain: | n/a | chr6:29343952-29343973 chr6:29343950-29343968 |
| 5 | CTCF | chr6:29343724-29344261 | HCT-116 | colon: | n/a | chr6:29343952-29343973 chr6:29343950-29343968 |
| 6 | RAD21 | chr6:29343644-29344183 | HCT-116 | colon: | n/a | chr6:29343951-29343970 |
| 7 | RAD21 | chr6:29343835-29344236 | HepG2 | liver: | n/a | chr6:29343951-29343970 |
| 8 | RAD21 | chr6:29343729-29344216 | H1-hESC | embryonic stem cell: | n/a | chr6:29343951-29343970 |
| 9 | RAD21 | chr6:29343749-29344193 | MCF-7 | breast: | n/a | chr6:29343951-29343970 |
| No data |
(count:3 , 50 per page) page:
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| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| OR12D3 | TF binding region |
rSNPs within LD-proxies of this variant (count:5)
| rs_ID | r2[population] |
|---|---|
| rs3117441 | 0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs5003264 | 0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs5003265 | 0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs5003266 | 1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs5003267 | 0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:7 , 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 | nsv601215 | chr6:28946920-29348297 | ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 45 gene(s) | inside rSNPs | diseases |
| 2 | nsv1018937 | chr6:28956136-29366175 | Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 38 gene(s) | inside rSNPs | diseases |
| 3 | nsv1020683 | chr6:29225146-29353408 | Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 8 gene(s) | inside rSNPs | diseases |
| 4 | nsv830624 | chr6:29274525-29445565 | Enhancers Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 11 gene(s) | inside rSNPs | diseases |
| 5 | nsv966676 | chr6:29326915-29365789 | Enhancers Active TSS | TF binding regionCpG islandChromatin interactive region | 3 gene(s) | inside rSNPs | diseases |
| 6 | nsv883527 | chr6:29342825-29354799 | Enhancers | TF binding regionCpG islandChromatin interactive region | 1 gene(s) | inside rSNPs | diseases |
| 7 | nsv519453 | chr6:29343355-29351873 | Enhancers | TF binding regionChromatin interactive region | 1 gene(s) | inside rSNPs | diseases |
| No data |
Chromatin state (count:0 , 50 per page) page:
| No data |
