Variant report
| Variant | rs12021612 |
|---|---|
| Chromosome Location | chr1:153449574-153449575 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:7)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:7 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr1:153361858..153365195-chr1:153447967..153452126,4 | MCF-7 | breast: | |
| 2 | chr1:153323483..153340048-chr1:153448254..153469845,61 | MCF-7 | breast: | |
| 3 | chr1:153443878..153448578-chr1:153449187..153452566,7 | MCF-7 | breast: | |
| 4 | chr1:153449114..153453479-chr1:153459428..153463150,4 | MCF-7 | breast: | |
| 5 | chr1:153366957..153368631-chr1:153449404..153450956,2 | MCF-7 | breast: | |
| 6 | chr1:153445670..153449598-chr1:153450178..153453743,4 | K562 | blood: | |
| 7 | chr1:153447398..153450153-chr1:153455745..153457768,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000163220 | Chromatin interaction |
| ENSG00000143546 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:16)
| rs_ID | r2[population] |
|---|---|
| rs11205297 | 0.87[EUR][1000 genomes] |
| rs12022550 | 1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs12024114 | 1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs12025638 | 1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs12044034 | 0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs12047203 | 0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs12047494 | 0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs16835332 | 1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs16835339 | 0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs2339695 | 1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs28696717 | 0.84[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs2986209 | 0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs3014848 | 0.97[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs55703007 | 0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs56009204 | 0.89[ASN][1000 genomes] |
| rs72708789 | 0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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 | nsv1010488 | chr1:152901263-153670972 | Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 236 gene(s) | inside rSNPs | diseases |
| 2 | nsv535171 | chr1:152901263-153670972 | Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 236 gene(s) | inside rSNPs | diseases |
| 3 | nsv533877 | chr1:152923645-153468131 | Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 56 gene(s) | inside rSNPs | diseases |
| 4 | nsv1002705 | chr1:153307852-153525589 | Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 152 gene(s) | inside rSNPs | diseases |
| 5 | nsv831603 | chr1:153405842-153576143 | Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 148 gene(s) | inside rSNPs | diseases |
| 6 | nsv1007306 | chr1:153413827-153541798 | Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 146 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:153448200-153450600 | Weak transcription | Placenta Amnion | Placenta Amnion |
| 2 | chr1:153448400-153450600 | Weak transcription | H1 BMP4 Derived Trophoblast Cultured Cells | ES cell derived |
| 3 | chr1:153448400-153450600 | Weak transcription | Fetal Heart | heart |
