Variant report
| Variant | rs12528446 |
|---|---|
| Chromosome Location | chr6:38673956-38673957 |
| allele | C/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:2)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:2 , 50 per page) page:
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| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | POLR2A | chr6:38673749-38674093 | H1-neurons | neurons: | n/a | n/a |
| 2 | POLR2A | chr6:38673701-38674131 | H1-neurons | neurons: | n/a | n/a |
| No data |
(count:1 , 50 per page) page:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr6:38670615..38673305-chr6:38673459..38675374,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| GLO1 | TF binding region |
| ENSG00000124767 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:18)
| rs_ID | r2[population] |
|---|---|
| rs10484855 | 1.00[YRI][hapmap] |
| rs12524113 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs12524122 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs12526818 | 1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes] |
| rs12527476 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs12529780 | 0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs12660979 | 0.84[AMR][1000 genomes] |
| rs12661103 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs12664739 | 1.00[CEU][hapmap];0.80[AMR][1000 genomes] |
| rs13191302 | 1.00[YRI][hapmap] |
| rs13196356 | 0.84[ASN][1000 genomes] |
| rs13196708 | 1.00[YRI][hapmap] |
| rs13198900 | 1.00[YRI][hapmap] |
| rs13203443 | 1.00[YRI][hapmap] |
| rs13217234 | 1.00[YRI][hapmap] |
| rs17544311 | 1.00[YRI][hapmap] |
| rs2277109 | 0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs34760807 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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 | nsv1021991 | chr6:37893949-38738720 | Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 20 gene(s) | inside rSNPs | diseases |
| 2 | nsv885817 | chr6:38036420-39019503 | Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 26 gene(s) | inside rSNPs | diseases |
| 3 | esv2758049 | chr6:38588969-38711085 | Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 11 gene(s) | inside rSNPs | diseases |
| 4 | esv2759421 | chr6:38588969-38711085 | Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 11 gene(s) | inside rSNPs | diseases |
| 5 | nsv427754 | chr6:38588969-38711085 | Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 11 gene(s) | inside rSNPs | diseases |
| 6 | nsv428144 | chr6:38588969-38711085 | Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 11 gene(s) | inside rSNPs | diseases |
| 7 | nsv830642 | chr6:38645056-38800657 | Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 12 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr6:38671400-38675000 | Weak transcription | Right Atrium | heart |
| 2 | chr6:38671400-38676000 | Weak transcription | HUVEC | blood vessel |
| 3 | chr6:38672000-38678400 | Weak transcription | Fetal Kidney | kidney |
