Variant report
| Variant | rs3741845 |
|---|---|
| Chromosome Location | chr12:10962115-10962116 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- 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 |
| No data |
(count:1 , 50 per page) page:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr12:10961808..10964056-chr12:11322515..11324346,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000256537 | Chromatin interaction |
| ENSG00000111215 | Chromatin interaction |
| ENSG00000256712 | Chromatin interaction |
| ENSG00000212127 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:15)
| rs_ID | r2[population] |
|---|---|
| rs10743925 | 0.93[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs10743926 | 0.93[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs10772365 | 0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes] |
| rs10845218 | 0.86[AMR][1000 genomes];0.84[EUR][1000 genomes] |
| rs10845219 | 0.86[AMR][1000 genomes];0.84[EUR][1000 genomes] |
| rs1548803 | 0.96[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs1838344 | 0.94[ASN][1000 genomes] |
| rs1838346 | 0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs2588350 | 0.89[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes] |
| rs3906863 | 0.86[AMR][1000 genomes];0.83[EUR][1000 genomes] |
| rs4262797 | 0.90[AMR][1000 genomes];0.91[EUR][1000 genomes] |
| rs4763216 | 0.86[AMR][1000 genomes];0.83[EUR][1000 genomes] |
| rs615239 | 0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs655046 | 0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs689118 | 0.85[EUR][1000 genomes];0.88[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1049362 | chr12:10893573-11018850 | Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 14 gene(s) | inside rSNPs | diseases |
| 2 | nsv898776 | chr12:10909412-11032045 | Genic enhancers Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 13 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:13)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs3741845 | RP11-434C1.1 | cis | Muscle Skeletal | GTEx |
| rs3741845 | RP11-785H5.1 | cis | Thyroid | GTEx |
| rs3741845 | TAS2R14 | cis | Artery Tibial | GTEx |
| rs3741845 | RP11-434C1.1 | cis | Artery Tibial | GTEx |
| rs3741845 | PRR4 | cis | Artery Tibial | GTEx |
| rs3741845 | PRR4 | cis | Esophagus Muscularis | GTEx |
| rs3741845 | PRR4 | cis | Thyroid | GTEx |
| rs3741845 | TAS2R14 | cis | Esophagus Muscularis | GTEx |
| rs3741845 | RP11-434C1.1 | cis | lung | GTEx |
| rs3741845 | PRR4 | cis | Muscle Skeletal | GTEx |
| rs3741845 | PRR4 | cis | lymphoblastoid | seeQTL |
| rs3741845 | PRR4 | cis | Heart Left Ventricle | GTEx |
| rs3741845 | PRR4 | cis | lung | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr12:10961200-10962200 | Enhancers | H9 Derived Neuron Cultured Cells | ES cell derived |
| 2 | chr12:10961400-10962600 | Enhancers | hESC Derived CD184+ Endoderm Cultured Cells | ES cell derived |
