Variant report
| Variant | rs3126090 |
|---|---|
| Chromosome Location | chr1:152306513-152306514 |
| 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:22)
| rs_ID | r2[population] |
|---|---|
| rs13375087 | 1.00[JPT][hapmap] |
| rs13375665 | 0.83[ASN][1000 genomes] |
| rs16833966 | 0.83[ASN][1000 genomes] |
| rs16834012 | 0.83[ASN][1000 genomes] |
| rs17359691 | 0.83[ASN][1000 genomes] |
| rs1858480 | 0.87[ASW][hapmap];0.82[YRI][hapmap] |
| rs1858481 | 0.82[ASW][hapmap];0.84[LWK][hapmap];0.90[MKK][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes] |
| rs1858482 | 0.87[ASW][hapmap];0.82[YRI][hapmap] |
| rs2338555 | 0.83[YRI][hapmap] |
| rs3120656 | 0.84[AMR][1000 genomes] |
| rs3126065 | 0.81[MKK][hapmap] |
| rs3126066 | 1.00[YRI][hapmap] |
| rs3126082 | 0.84[AMR][1000 genomes] |
| rs3126085 | 0.86[ASW][hapmap];0.82[YRI][hapmap] |
| rs3126087 | 0.82[ASW][hapmap];0.83[LWK][hapmap];0.90[MKK][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes] |
| rs3126088 | 0.87[ASW][hapmap];0.82[YRI][hapmap] |
| rs3126093 | 1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes] |
| rs3134871 | 0.82[ASW][hapmap];0.85[LWK][hapmap];0.90[MKK][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes] |
| rs3134872 | 0.81[MKK][hapmap];0.84[AMR][1000 genomes] |
| rs3134873 | 0.84[AMR][1000 genomes];1.00[ASN][1000 genomes] |
| rs72477395 | 0.83[ASN][1000 genomes] |
| rs7354940 | 0.83[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 | nsv1014095 | chr1:152104486-152454591 | Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 28 gene(s) | inside rSNPs | diseases |
| 2 | nsv1005472 | chr1:152247763-152443448 | Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 23 gene(s) | inside rSNPs | diseases |
| 3 | nsv535161 | chr1:152247763-152443448 | Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 23 gene(s) | inside rSNPs | diseases |
| 4 | nsv998298 | chr1:152288685-152319877 | Enhancers Weak transcription Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 12 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs3126090 | HRNR | cis | lung | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:152286600-152322200 | Weak transcription | Ovary | ovary |
| 2 | chr1:152302000-152309600 | Weak transcription | Aorta | Aorta |
