Variant report
| Variant | rs12192932 |
|---|---|
| Chromosome Location | chr6:25911502-25911503 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:5)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:5 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr6:25910143..25913529-chr6:25915155..25917644,3 | K562 | blood: | |
| 2 | chr6:25894658..25897194-chr6:25908960..25911635,2 | MCF-7 | breast: | |
| 3 | chr6:25902877..25904563-chr6:25909751..25912391,2 | K562 | blood: | |
| 4 | chr6:25909186..25911727-chr6:25964970..25966788,2 | K562 | blood: | |
| 5 | chr6:25899487..25901860-chr6:25910075..25912188,3 | K562 | blood: |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:14)
| rs_ID | r2[population] |
|---|---|
| rs10456326 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs10484432 | 0.81[AFR][1000 genomes];0.85[EUR][1000 genomes] |
| rs10807004 | 1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs12192649 | 0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes] |
| rs12199626 | 0.84[EUR][1000 genomes] |
| rs12201678 | 0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes] |
| rs12204800 | 0.81[AFR][1000 genomes] |
| rs12207059 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs17586946 | 0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs2009610 | 0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs41266791 | 0.81[AFR][1000 genomes] |
| rs59306177 | 0.81[AFR][1000 genomes];0.87[AMR][1000 genomes] |
| rs6907991 | 0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs8384 | 0.81[AFR][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 | nsv1029920 | chr6:25638507-26585842 | Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 1215 gene(s) | inside rSNPs | diseases |
| 2 | nsv538162 | chr6:25638507-26585842 | Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 1215 gene(s) | inside rSNPs | diseases |
| 3 | nsv1030351 | chr6:25813178-26352046 | Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 1189 gene(s) | inside rSNPs | diseases |
| 4 | nsv1023453 | chr6:25853830-26528250 | Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 1201 gene(s) | inside rSNPs | diseases |
| 5 | nsv1025237 | chr6:25874326-26280867 | Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 1166 gene(s) | inside rSNPs | diseases |
| 6 | nsv538163 | chr6:25874326-26280867 | Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 1166 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:5)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs12192932 | U91328.19 | cis | Muscle Skeletal | GTEx |
| rs12192932 | U91328.19 | cis | Esophagus Mucosa | GTEx |
| rs12192932 | U91328.19 | cis | Thyroid | GTEx |
| rs12192932 | U91328.19 | cis | Nerve Tibial | GTEx |
| rs12192932 | U91328.19 | cis | Artery Tibial | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr6:25908000-25915600 | Enhancers | HepG2 | liver |
| 2 | chr6:25910400-25912000 | Enhancers | K562 | blood |
| 3 | chr6:25910800-25911800 | Weak transcription | Liver | Liver |
