Variant report
| Variant | rs1949007 |
|---|---|
| Chromosome Location | chr4:171957000-171957001 |
| 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:25)
| rs_ID | r2[population] |
|---|---|
| rs10010024 | 0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs12648447 | 0.88[TSI][hapmap] |
| rs12651692 | 0.80[AFR][1000 genomes] |
| rs13148831 | 0.80[EUR][1000 genomes] |
| rs1508297 | 0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs1911811 | 0.83[AFR][1000 genomes] |
| rs1949006 | 0.85[AFR][1000 genomes] |
| rs2048201 | 0.80[EUR][1000 genomes] |
| rs2332085 | 0.80[EUR][1000 genomes] |
| rs2332086 | 0.80[EUR][1000 genomes] |
| rs2332087 | 0.82[EUR][1000 genomes] |
| rs25510 | 0.88[TSI][hapmap] |
| rs25511 | 0.89[TSI][hapmap] |
| rs25512 | 0.89[TSI][hapmap] |
| rs28611223 | 0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs28706078 | 0.82[AFR][1000 genomes] |
| rs56223128 | 0.83[EUR][1000 genomes] |
| rs56886621 | 0.80[EUR][1000 genomes] |
| rs61012267 | 0.80[EUR][1000 genomes] |
| rs61448487 | 0.80[EUR][1000 genomes] |
| rs6419980 | 0.80[EUR][1000 genomes] |
| rs6811103 | 0.86[TSI][hapmap] |
| rs6811337 | 0.89[TSI][hapmap] |
| rs6827582 | 0.80[EUR][1000 genomes] |
| rs7340816 | 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 | nsv881345 | chr4:171673765-172228547 | Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA | 17 gene(s) | inside rSNPs | diseases |
| 2 | nsv1018793 | chr4:171808272-172395180 | Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA | 16 gene(s) | inside rSNPs | diseases |
| 3 | nsv881662 | chr4:171842726-171957000 | Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS | TF binding regionChromatin interactive region | 2 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs1949007 | NEK1 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr4:171953600-171960600 | Weak transcription | Primary hematopoietic stem cells short term culture | blood |
| 2 | chr4:171956800-171957000 | Enhancers | H1 BMP4 Derived Mesendoderm Cultured Cells | ES cell derived |
