Variant report
| Variant | rs17099866 |
|---|---|
| Chromosome Location | chr12:64233260-64233261 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:139)
- CpG islands (count:0)
- Chromatin interactive region (count:8)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
(count:8 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr12:64231966..64234951-chr12:64236615..64238882,2 | MCF-7 | breast: | |
| 2 | chr12:64232886..64234110-chr12:64649608..64650623,12 | MCF-7 | breast: | |
| 3 | chr12:64232878..64233896-chr12:64649649..64650593,6 | MCF-7 | breast: | |
| 4 | chr12:64219747..64220434-chr12:64233020..64233910,3 | MCF-7 | breast: | |
| 5 | chr12:64232809..64233732-chr12:64630031..64630616,2 | MCF-7 | breast: | |
| 6 | chr12:64232868..64233765-chr12:64667261..64668056,2 | MCF-7 | breast: | |
| 7 | chr12:64232967..64233604-chr12:64648677..64649365,2 | MCF-7 | breast: | |
| 8 | chr12:64232788..64233929-chr12:64575209..64576068,7 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| SRGAP1 | TF binding region |
| ENSG00000196935 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:51)
| rs_ID | r2[population] |
|---|---|
| rs10506464 | 0.83[ASN][1000 genomes] |
| rs11175184 | 0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs11175185 | 0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs11175188 | 0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs11175189 | 0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs11175197 | 0.86[ASN][1000 genomes] |
| rs11833808 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs11835034 | 0.87[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs12228199 | 0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs12229790 | 0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs12579795 | 0.82[ASN][1000 genomes] |
| rs2335884 | 0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs35143986 | 0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs4072758 | 0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs55642517 | 0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs55655348 | 0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs55760535 | 0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs55907605 | 0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs55930806 | 0.85[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs56028204 | 0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs56080061 | 0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs56264182 | 0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs58424013 | 0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs59063572 | 0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs60031756 | 0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs6581509 | 0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs6581510 | 0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs66856673 | 0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs67401817 | 0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs67684483 | 0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs67830727 | 0.85[EUR][1000 genomes];0.85[ASN][1000 genomes] |
| rs67880496 | 0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs67892056 | 0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs67993208 | 0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs68188132 | 0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs7136130 | 0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs7294327 | 0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs7301437 | 0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes] |
| rs7302672 | 0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs7304340 | 0.85[EUR][1000 genomes];0.85[ASN][1000 genomes] |
| rs7305893 | 0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs7307108 | 0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs7308850 | 0.81[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs7310327 | 0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs7310329 | 0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs7310575 | 0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs7311611 | 0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs73313479 | 0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs73315321 | 0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs73315365 | 0.87[ASN][1000 genomes] |
| rs7953208 | 0.87[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1046836 | chr12:63392391-64377169 | Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 41 gene(s) | inside rSNPs | diseases |
| 2 | esv2759905 | chr12:63901801-64252172 | Bivalent Enhancer Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 20 gene(s) | inside rSNPs | diseases |
| 3 | esv2758312 | chr12:63910416-64252172 | Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 20 gene(s) | inside rSNPs | diseases |
| 4 | esv2751110 | chr12:63939733-64274680 | Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 24 gene(s) | inside rSNPs | diseases |
| 5 | nsv832441 | chr12:64063776-64252172 | Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 19 gene(s) | inside rSNPs | diseases |
| 6 | nsv746 | chr12:64189444-64234966 | Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 10 gene(s) | inside rSNPs | diseases |
| 7 | nsv832442 | chr12:64228071-64442771 | Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 18 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr12:64216200-64237000 | Weak transcription | Foreskin Fibroblast Primary Cells skin02 | Skin |
| 2 | chr12:64228200-64235800 | Enhancers | Fetal Brain Male | brain |
| 3 | chr12:64230600-64237000 | Weak transcription | Right Atrium | heart |
| 4 | chr12:64230800-64237000 | Weak transcription | Brain Germinal Matrix | brain |
| 5 | chr12:64231000-64237000 | Weak transcription | H9 Derived Neuronal Progenitor Cultured Cells | ES cell derived |
| 6 | chr12:64232200-64236800 | Weak transcription | Fetal Brain Female | brain |
