Variant report
| Variant | rs7966478 |
|---|---|
| Chromosome Location | chr12:120377392-120377393 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:4)
- LncRNA region (count:1)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:4 , 50 per page) page:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr12:120375794..120377491-chr12:120554770..120557327,2 | MCF-7 | breast: | |
| 2 | chr12:120376864..120378472-chr12:120729322..120731288,2 | MCF-7 | breast: | |
| 3 | chr12:120375923..120377476-chr12:120425555..120428485,2 | MCF-7 | breast: | |
| 4 | chr12:120376974..120380203-chr12:120515998..120518791,3 | MCF-7 | breast: |
(count:1 , 50 per page) page:
1
| No. | lncRNA name | Chromosome Location | lncRNA alias |
|---|---|---|---|
| 1 | lnc-CCDC64-2 | chr12:120377270-120377404 | NONHSAT031098 |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000135127 | Chromatin interaction |
| ENSG00000200795 | Chromatin interaction |
| ENSG00000202538 | Chromatin interaction |
| ENSG00000111737 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:14)
| rs_ID | r2[population] |
|---|---|
| rs11612544 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs11614631 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs12818102 | 0.96[AMR][1000 genomes];0.99[EUR][1000 genomes] |
| rs12819458 | 0.82[AMR][1000 genomes];0.82[ASN][1000 genomes] |
| rs12819623 | 0.83[AMR][1000 genomes];0.82[ASN][1000 genomes] |
| rs17412729 | 0.94[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap] |
| rs35656829 | 0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs3858717 | 0.96[CEU][hapmap] |
| rs4767865 | 0.94[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap] |
| rs7297338 | 0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs73217374 | 0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs7964604 | 0.87[CHB][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes] |
| rs7968264 | 0.94[CHB][hapmap] |
| rs7972879 | 0.97[AMR][1000 genomes];0.99[EUR][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 | nsv455727 | chr12:120259679-120420670 | Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 13 gene(s) | inside rSNPs | diseases |
| 2 | nsv560397 | chr12:120259679-120420670 | Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 13 gene(s) | inside rSNPs | diseases |
| 3 | nsv510575 | chr12:120303163-120437490 | Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 16 gene(s) | inside rSNPs | diseases |
| 4 | esv3525916 | chr12:120345352-120665045 | Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking 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 | 99 gene(s) | inside rSNPs | diseases |
| 5 | esv3525917 | chr12:120345352-120665045 | Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 99 gene(s) | inside rSNPs | diseases |
| 6 | nsv455728 | chr12:120355563-120396295 | Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats | TF binding regionChromatin interactive regionlncRNA | 5 gene(s) | inside rSNPs | diseases |
| 7 | nsv560398 | chr12:120355563-120396295 | Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer | TF binding regionChromatin interactive regionlncRNA | 5 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs7966478 | CCDC64 | cis | parietal | SCAN |
| rs7966478 | POP5 | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr12:120369600-120378200 | Weak transcription | Hela-S3 | cervix |
