Variant report
| Variant | rs6550842 |
|---|---|
| Chromosome Location | chr3:24099794-24099795 |
| allele | C/T |
| 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:21)
| rs_ID | r2[population] |
|---|---|
| rs11925334 | 0.93[EUR][1000 genomes];0.81[ASN][1000 genomes] |
| rs1511536 | 0.99[EUR][1000 genomes] |
| rs1511537 | 0.84[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs1511540 | 0.92[EUR][1000 genomes] |
| rs2063480 | 0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs2360958 | 0.91[EUR][1000 genomes] |
| rs2360959 | 0.91[EUR][1000 genomes] |
| rs34312629 | 0.87[ASN][1000 genomes] |
| rs4416337 | 0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs4561770 | 0.86[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs4624512 | 0.99[EUR][1000 genomes] |
| rs60226192 | 0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs6550840 | 0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs6550846 | 0.92[EUR][1000 genomes] |
| rs6765461 | 0.95[EUR][1000 genomes] |
| rs6777075 | 0.99[EUR][1000 genomes] |
| rs6781758 | 0.94[EUR][1000 genomes] |
| rs7612158 | 0.96[EUR][1000 genomes] |
| rs7623641 | 0.86[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs7634184 | 0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs7639580 | 0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv533980 | chr3:23445901-24311972 | ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 64 gene(s) | inside rSNPs | diseases |
| 2 | nsv834638 | chr3:23963860-24117191 | Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 19 gene(s) | inside rSNPs | diseases |
| 3 | nsv834639 | chr3:24037113-24233925 | Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 13 gene(s) | inside rSNPs | diseases |
| 4 | nsv1004037 | chr3:24064777-24143719 | Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 6 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs6550842 | NR1D2 | Cis_1M | lymphoblastoid | RTeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr3:24090800-24101400 | Weak transcription | NHLF | lung |
