Variant report
| Variant | rs1898153 |
|---|---|
| Chromosome Location | chr1:242292794-242292795 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:16)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:16 , 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 | chr1:242292443-242292869 | MCF-7 | breast: | n/a | chr1:242292614-242292633 chr1:242292616-242292628 |
| 2 | CTCF | chr1:242292369-242292846 | HCT-116 | colon: | n/a | chr1:242292611-242292632 |
| 3 | CTCF | chr1:242292376-242292872 | MCF-7 | breast: | n/a | chr1:242292611-242292632 |
| 4 | RAD21 | chr1:242292366-242292850 | HCT-116 | colon: | n/a | chr1:242292614-242292633 chr1:242292616-242292628 |
| 5 | RAD21 | chr1:242292370-242292857 | A549 | lung: | n/a | chr1:242292614-242292633 chr1:242292616-242292628 |
| 6 | RAD21 | chr1:242292325-242292856 | HCT-116 | colon: | n/a | chr1:242292614-242292633 chr1:242292616-242292628 |
| 7 | CTCF | chr1:242292424-242292797 | GM12878 | blood: | n/a | chr1:242292611-242292632 |
| 8 | RAD21 | chr1:242292327-242292925 | MCF-7 | breast: | n/a | chr1:242292614-242292633 chr1:242292616-242292628 |
| 9 | STAT3 | chr1:242292748-242293132 | MCF10A-Er-Src | breast: | n/a | n/a |
| 10 | RAD21 | chr1:242292394-242292802 | H1-hESC | embryonic stem cell: | n/a | chr1:242292614-242292633 chr1:242292616-242292628 |
| 11 | RAD21 | chr1:242292307-242292860 | H1-hESC | embryonic stem cell: | n/a | chr1:242292614-242292633 chr1:242292616-242292628 |
| 12 | CTCF | chr1:242292438-242292811 | H1-hESC | embryonic stem cell: | n/a | chr1:242292611-242292632 |
| 13 | RAD21 | chr1:242292355-242292839 | H1-hESC | embryonic stem cell: | n/a | chr1:242292614-242292633 chr1:242292616-242292628 |
| 14 | CUX1 | chr1:242292651-242292839 | K562 | blood: | n/a | n/a |
| 15 | RAD21 | chr1:242292232-242292979 | SK-N-SH | brain: | n/a | chr1:242292614-242292633 chr1:242292616-242292628 |
| 16 | CTCF | chr1:242292368-242292927 | A549 | lung: | n/a | chr1:242292611-242292632 |
| No data |
(count:1 , 50 per page) page:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr1:242182508..242183674-chr1:242292156..242293080,6 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| RNA5SP81 | TF binding region |
rSNPs within LD-proxies of this variant (count:8)
| rs_ID | r2[population] |
|---|---|
| rs2252347 | 0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs2252440 | 0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs2252441 | 0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs2574669 | 0.86[AMR][1000 genomes];0.86[ASN][1000 genomes] |
| rs2636252 | 0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs2800772 | 0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs2840614 | 0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs6663013 | 0.83[AMR][1000 genomes];0.80[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:11 , 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 | nsv873372 | chr1:241690554-242438293 | Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 40 gene(s) | inside rSNPs | diseases |
| 2 | nsv948409 | chr1:241830086-242489705 | Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 26 gene(s) | inside rSNPs | diseases |
| 3 | esv2750830 | chr1:242025098-242303357 | Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 11 gene(s) | inside rSNPs | diseases |
| 4 | esv2750831 | chr1:242025098-242332959 | Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 12 gene(s) | inside rSNPs | diseases |
| 5 | nsv1002309 | chr1:242042242-242295635 | Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 10 gene(s) | inside rSNPs | diseases |
| 6 | nsv468672 | chr1:242201247-242555949 | Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 10 gene(s) | inside rSNPs | diseases |
| 7 | nsv470788 | chr1:242201247-242555949 | Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 10 gene(s) | inside rSNPs | diseases |
| 8 | nsv549462 | chr1:242201247-242555949 | Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 10 gene(s) | inside rSNPs | diseases |
| 9 | nsv528016 | chr1:242223399-242451350 | Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 7 gene(s) | inside rSNPs | diseases |
| 10 | nsv549463 | chr1:242265419-242856854 | Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 15 gene(s) | inside rSNPs | diseases |
| 11 | nsv998804 | chr1:242281003-242491362 | Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 5 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:242282200-242298600 | Weak transcription | Breast variant Human Mammary Epithelial Cells (vHMEC) | Breast |
| 2 | chr1:242292600-242295800 | Weak transcription | Brain Angular Gyrus | brain |
