Variant report
| Variant | rs61825663 |
|---|---|
| Chromosome Location | chr1:228741993-228741994 |
| allele | G/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:9)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:9 , 50 per page) page:
1
| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | TCF12 | chr1:228741241-228742791 | ECC-1 | luminal epithelium: | n/a | n/a |
| 2 | TCF12 | chr1:228741823-228742590 | ECC-1 | luminal epithelium: | n/a | n/a |
| 3 | TEAD4 | chr1:228741851-228742609 | ECC-1 | luminal epithelium: | n/a | n/a |
| 4 | ESR1 | chr1:228741838-228742119 | ECC-1 | luminal epithelium: | n/a | n/a |
| 5 | TEAD4 | chr1:228741831-228742331 | ECC-1 | luminal epithelium: | n/a | n/a |
| 6 | NFIC | chr1:228741823-228742670 | ECC-1 | luminal epithelium: | n/a | n/a |
| 7 | EP300 | chr1:228741844-228742310 | ECC-1 | luminal epithelium: | n/a | n/a |
| 8 | EP300 | chr1:228741231-228742773 | ECC-1 | luminal epithelium: | n/a | n/a |
| 9 | NFIC | chr1:228741801-228742155 | ECC-1 | luminal epithelium: | n/a | n/a |
| No data |
| No data |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| RNA5SP19 | TF binding region |
| DUSP5P1 | TF binding region |
rSNPs within LD-proxies of this variant (count:16)
| rs_ID | r2[population] |
|---|---|
| rs12028234 | 0.89[ASN][1000 genomes] |
| rs12044013 | 1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs12045742 | 0.90[AFR][1000 genomes];0.89[EUR][1000 genomes] |
| rs12046644 | 0.90[AFR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes] |
| rs12161195 | 0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs12161347 | 0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs12563568 | 0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs1925715 | 0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs1925723 | 1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs4344301 | 0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs61825664 | 0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs61827306 | 0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs61827315 | 0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs61827317 | 0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs61827321 | 1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs942850 | 0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | esv32853 | chr1:227880116-228806209 | Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 187 gene(s) | inside rSNPs | diseases |
| 2 | nsv1009891 | chr1:228450763-228742676 | Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 68 gene(s) | inside rSNPs | diseases |
| 3 | nsv1013500 | chr1:228459134-228849601 | Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 98 gene(s) | inside rSNPs | diseases |
| 4 | esv15299 | chr1:228716554-228744099 | Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh | TF binding regionCpG island | 2 gene(s) | inside rSNPs | diseases |
| 5 | nsv827075 | chr1:228716554-228783674 | Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive region | 28 gene(s) | inside rSNPs | diseases |
| 6 | nsv945355 | chr1:228716611-228784016 | Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive region | 29 gene(s) | inside rSNPs | diseases |
| No data |
Chromatin state (count:0 , 50 per page) page:
| No data |
