Variant report
| Variant | rs3113879 |
|---|---|
| Chromosome Location | chr4:48002327-48002328 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
| No data |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:75)
| rs_ID | r2[population] |
|---|---|
| rs10002498 | 1.00[ASN][1000 genomes] |
| rs10020447 | 1.00[ASN][1000 genomes] |
| rs1036681 | 1.00[ASN][1000 genomes] |
| rs10461075 | 0.81[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs11732840 | 1.00[ASN][1000 genomes] |
| rs11946535 | 1.00[ASN][1000 genomes] |
| rs12506026 | 1.00[ASN][1000 genomes] |
| rs12647189 | 1.00[ASN][1000 genomes] |
| rs13143926 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs1440222 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs1545200 | 1.00[ASN][1000 genomes] |
| rs1550444 | 1.00[ASN][1000 genomes] |
| rs1812964 | 1.00[ASN][1000 genomes] |
| rs188900 | 0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs1968542 | 1.00[ASN][1000 genomes] |
| rs1972883 | 1.00[ASN][1000 genomes] |
| rs1972884 | 1.00[ASN][1000 genomes] |
| rs2014934 | 1.00[ASN][1000 genomes] |
| rs2033895 | 1.00[ASN][1000 genomes] |
| rs2119204 | 1.00[ASN][1000 genomes] |
| rs2119207 | 1.00[ASN][1000 genomes] |
| rs2119208 | 1.00[ASN][1000 genomes] |
| rs224801 | 0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs2352456 | 1.00[ASN][1000 genomes] |
| rs2352457 | 1.00[ASN][1000 genomes] |
| rs2352463 | 1.00[ASN][1000 genomes] |
| rs2352466 | 1.00[ASN][1000 genomes] |
| rs2581496 | 0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs28464733 | 1.00[ASN][1000 genomes] |
| rs2882950 | 1.00[ASN][1000 genomes] |
| rs3113877 | 0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs3113880 | 1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs321625 | 0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs321639 | 0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs321640 | 0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs321641 | 0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs321647 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs321649 | 0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs3762858 | 1.00[ASN][1000 genomes] |
| rs3762859 | 1.00[ASN][1000 genomes] |
| rs3811761 | 1.00[ASN][1000 genomes] |
| rs3845160 | 1.00[ASN][1000 genomes] |
| rs4308343 | 1.00[ASN][1000 genomes] |
| rs4365692 | 1.00[ASN][1000 genomes] |
| rs4507330 | 1.00[ASN][1000 genomes] |
| rs4694868 | 1.00[ASN][1000 genomes] |
| rs4694871 | 1.00[ASN][1000 genomes] |
| rs4694878 | 1.00[ASN][1000 genomes] |
| rs4695287 | 1.00[ASN][1000 genomes] |
| rs4695302 | 1.00[ASN][1000 genomes] |
| rs4695309 | 1.00[ASN][1000 genomes] |
| rs4695312 | 1.00[ASN][1000 genomes] |
| rs6447596 | 1.00[ASN][1000 genomes] |
| rs6447599 | 1.00[ASN][1000 genomes] |
| rs6815975 | 1.00[ASN][1000 genomes] |
| rs6819506 | 1.00[ASN][1000 genomes] |
| rs6823572 | 1.00[ASN][1000 genomes] |
| rs6826190 | 1.00[ASN][1000 genomes] |
| rs6826909 | 1.00[ASN][1000 genomes] |
| rs6832334 | 1.00[ASN][1000 genomes] |
| rs6833320 | 1.00[ASN][1000 genomes] |
| rs6845451 | 1.00[ASN][1000 genomes] |
| rs707723 | 1.00[ASN][1000 genomes] |
| rs7668778 | 1.00[ASN][1000 genomes] |
| rs7670219 | 1.00[ASN][1000 genomes] |
| rs7672090 | 1.00[ASN][1000 genomes] |
| rs7690406 | 1.00[ASN][1000 genomes] |
| rs7690522 | 1.00[ASN][1000 genomes] |
| rs893861 | 1.00[ASN][1000 genomes] |
| rs893863 | 1.00[ASN][1000 genomes] |
| rs893864 | 1.00[ASN][1000 genomes] |
| rs920463 | 1.00[ASN][1000 genomes] |
| rs9291318 | 1.00[ASN][1000 genomes] |
| rs9291319 | 1.00[ASN][1000 genomes] |
| rs9995022 | 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 | esv3447039 | chr4:47822266-48285222 | Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 34 gene(s) | inside rSNPs | diseases |
| 2 | nsv1013947 | chr4:47915527-48052824 | Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 8 gene(s) | inside rSNPs | diseases |
| 3 | nsv537082 | chr4:47915527-48052824 | Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 8 gene(s) | inside rSNPs | diseases |
| 4 | nsv1006745 | chr4:47935250-48052824 | Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 6 gene(s) | inside rSNPs | diseases |
| 5 | nsv537083 | chr4:47935250-48052824 | Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 6 gene(s) | inside rSNPs | diseases |
| 6 | nsv1013163 | chr4:47977844-48022511 | Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 5 gene(s) | inside rSNPs | diseases |
| 7 | nsv537084 | chr4:47977844-48022511 | Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 5 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:4)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs3113879 | CNGA1 | cis | Esophagus Muscularis | GTEx |
| rs3113879 | CNGA1 | cis | Thyroid | GTEx |
| rs3113879 | CNGA1 | cis | Muscle Skeletal | GTEx |
| rs3113879 | CNGA1 | cis | Heart Left Ventricle | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr4:48001800-48003800 | Weak transcription | Liver | Liver |
