Variant report
| Variant | rs600237 |
|---|---|
| Chromosome Location | chr1:78682554-78682555 |
| 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:24)
| rs_ID | r2[population] |
|---|---|
| rs10493608 | 0.92[ASN][1000 genomes] |
| rs10873966 | 0.80[EUR][1000 genomes] |
| rs10873967 | 0.90[ASN][1000 genomes] |
| rs12095545 | 0.87[EUR][1000 genomes] |
| rs1323094 | 0.80[EUR][1000 genomes] |
| rs1323096 | 0.90[ASN][1000 genomes] |
| rs1323098 | 0.91[ASN][1000 genomes] |
| rs1770303 | 0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs1770311 | 0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs1770313 | 0.90[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs2025611 | 0.80[EUR][1000 genomes] |
| rs2146612 | 0.80[EUR][1000 genomes] |
| rs4650382 | 0.90[EUR][1000 genomes] |
| rs593113 | 0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs616518 | 0.82[EUR][1000 genomes] |
| rs637650 | 0.80[EUR][1000 genomes] |
| rs638232 | 0.91[EUR][1000 genomes] |
| rs653899 | 0.82[EUR][1000 genomes] |
| rs658377 | 0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs669357 | 0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs669764 | 0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs671229 | 0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs672620 | 0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs689374 | 0.80[EUR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1013008 | chr1:78463173-78958701 | Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 72 gene(s) | inside rSNPs | diseases |
| 2 | nsv535012 | chr1:78463173-78958701 | Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 72 gene(s) | inside rSNPs | diseases |
| 3 | nsv871835 | chr1:78528803-79501129 | Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 28 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs600237 | NEXN | Cis_1M | lymphoblastoid | RTeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:78680800-78688600 | Weak transcription | Breast variant Human Mammary Epithelial Cells (vHMEC) | Breast |
| 2 | chr1:78681200-78683200 | Weak transcription | hESC Derived CD184+ Endoderm Cultured Cells | ES cell derived |
