Variant report
| Variant | rs7029589 |
|---|---|
| Chromosome Location | chr9:105279735-105279736 |
| allele | G/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:1)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
| No data |
(count:1 , 50 per page) page:
1
| No. | lncRNA name | Chromosome Location | lncRNA alias |
|---|---|---|---|
| 1 | lnc-C9orf107-4 | chr9:105277486-105280590 | NONHSAT133766 |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:8)
| rs_ID | r2[population] |
|---|---|
| rs10512298 | 0.80[EUR][1000 genomes] |
| rs10760895 | 0.80[ASN][1000 genomes] |
| rs12004032 | 1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs4743553 | 0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes] |
| rs7042651 | 0.90[EUR][1000 genomes] |
| rs7854645 | 0.80[ASN][1000 genomes] |
| rs7873462 | 0.89[CEU][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes] |
| rs7873568 | 0.88[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 | nsv893650 | chr9:105198550-105292037 | Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats | TF binding regionChromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | diseases |
| 2 | nsv1040886 | chr9:105246682-105296385 | Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats | TF binding regionChromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | diseases |
| 3 | nsv1055040 | chr9:105264905-105355578 | Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription | TF binding regionChromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:3)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs7029589 | NCBP1 | cis | cerebellum | SCAN |
| rs7029589 | TEX10 | cis | cerebellum | SCAN |
| rs7029589 | XPA | cis | parietal | SCAN |
Chromatin state (count:0 , 50 per page) page:
| No data |
