Variant report
| Variant | rs963878 |
|---|---|
| Chromosome Location | chr12:11639727-11639728 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:260)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
(count:1 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr12:10923542..10924154-chr12:11639667..11640247,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000255790 | TF binding region |
rSNPs within LD-proxies of this variant (count:16)
| rs_ID | r2[population] |
|---|---|
| rs1005265 | 1.00[CEU][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs10743960 | 0.96[YRI][hapmap];0.92[AFR][1000 genomes] |
| rs10772478 | 1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes] |
| rs17209646 | 1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs1974695 | 0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes] |
| rs2908831 | 0.90[AFR][1000 genomes] |
| rs2908836 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs2908838 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs2951770 | 1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs2951775 | 0.84[YRI][hapmap];0.84[AFR][1000 genomes] |
| rs2951783 | 0.96[YRI][hapmap];0.84[AFR][1000 genomes] |
| rs2965703 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs4237932 | 0.96[YRI][hapmap];0.93[AFR][1000 genomes] |
| rs7342388 | 0.81[YRI][hapmap];0.81[AFR][1000 genomes] |
| rs888125 | 0.88[EUR][1000 genomes];0.83[ASN][1000 genomes] |
| rs888127 | 0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[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 | esv2758294 | chr12:10969620-11714921 | Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 52 gene(s) | inside rSNPs | diseases |
| 2 | esv2759879 | chr12:10969620-11714921 | Genic enhancers Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 52 gene(s) | inside rSNPs | diseases |
| 3 | nsv428272 | chr12:11069845-11714921 | Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 47 gene(s) | inside rSNPs | diseases |
| 4 | nsv557572 | chr12:11575570-11693121 | Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
| 5 | nsv469112 | chr12:11575570-11711690 | Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 8 gene(s) | inside rSNPs | diseases |
| 6 | nsv557573 | chr12:11575570-11711690 | Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 8 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr12:11639200-11640000 | Enhancers | Primary T helper cells PMA-I stimulated | -- |
| 2 | chr12:11639400-11639800 | Active TSS | Brain Hippocampus Middle | brain |
| 3 | chr12:11639400-11640000 | Enhancers | ES-WA7 Cell Line | embryonic stem cell |
| 4 | chr12:11639400-11640000 | Weak transcription | H9 Cell Line | embryonic stem cell |
| 5 | chr12:11639400-11640000 | Enhancers | Primary B cells from peripheral blood | blood |
| 6 | chr12:11639400-11640000 | Enhancers | Primary hematopoietic stem cells G-CSF-mobilized Male | -- |
