Variant report
| Variant | rs16982990 |
|---|---|
| Chromosome Location | chr20:21790982-21790983 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:1 , 50 per page) page:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr20:21788351..21791666-chr20:22086552..22088383,19 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:12)
| rs_ID | r2[population] |
|---|---|
| rs11906825 | 0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs16983003 | 0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes] |
| rs16983004 | 0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs55744573 | 0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs55920747 | 0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs56338907 | 0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs56339958 | 0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes] |
| rs6035953 | 0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes] |
| rs6047633 | 0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs6047637 | 0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs62217507 | 0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes] |
| rs7264919 | 0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page:
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| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1058137 | chr20:21549350-22295051 | Weak transcription Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 17 gene(s) | inside rSNPs | diseases |
| 2 | nsv912814 | chr20:21703615-21946928 | Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS | TF binding regionChromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
| 3 | nsv1066350 | chr20:21758674-21792596 | Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats | Chromatin interactive region | n/a | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs16982990 | PAX1 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr20:21790000-21791000 | Enhancers | iPS DF 19.11 Cell Line | embryonic stem cell |
