Variant report
| Variant | rs17260245 |
|---|---|
| Chromosome Location | chr1:209411025-209411026 |
| 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:29)
| rs_ID | r2[population] |
|---|---|
| rs10494919 | 0.84[EUR][1000 genomes] |
| rs1507332 | 0.87[EUR][1000 genomes] |
| rs1507333 | 0.95[EUR][1000 genomes] |
| rs1553623 | 0.87[EUR][1000 genomes] |
| rs17188002 | 0.82[AFR][1000 genomes] |
| rs17188030 | 1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs17260224 | 1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs2055700 | 0.95[EUR][1000 genomes] |
| rs2788153 | 0.88[EUR][1000 genomes] |
| rs2800930 | 1.00[CEU][hapmap];0.95[EUR][1000 genomes] |
| rs4504891 | 0.93[EUR][1000 genomes] |
| rs56805778 | 0.82[AFR][1000 genomes] |
| rs59658508 | 0.81[AMR][1000 genomes];0.93[EUR][1000 genomes] |
| rs6661882 | 0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs6671102 | 0.84[EUR][1000 genomes] |
| rs6673758 | 0.81[AMR][1000 genomes] |
| rs6681844 | 0.93[EUR][1000 genomes] |
| rs6687960 | 1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs73085915 | 0.85[AFR][1000 genomes] |
| rs73085919 | 0.84[AMR][1000 genomes];0.93[EUR][1000 genomes] |
| rs73085921 | 0.84[AMR][1000 genomes];0.90[EUR][1000 genomes] |
| rs73085926 | 0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs73085932 | 0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs73085944 | 0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes] |
| rs73085950 | 0.84[AMR][1000 genomes];0.93[EUR][1000 genomes] |
| rs7533402 | 1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs906352 | 0.92[EUR][1000 genomes] |
| rs949488 | 0.95[EUR][1000 genomes] |
| rs976940 | 0.87[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 | nsv832481 | chr1:209371276-209540333 | Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 9 gene(s) | inside rSNPs | diseases |
| 2 | nsv832492 | chr1:209383771-209589312 | Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 9 gene(s) | inside rSNPs | diseases |
| 3 | esv1008555 | chr1:209409577-209416496 | Strong transcription Weak transcription Enhancers | Chromatin interactive region | n/a | inside rSNPs | diseases |
mRNA abundance (count:4)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs17260245 | SNORD116-29 | trans | lymphoblastoid | seeQTL |
| rs17260245 | ARC | trans | brain | seeQTL |
| rs17260245 | PTGS2 | trans | brain | seeQTL |
| rs17260245 | EGR2 | trans | brain | seeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:209409800-209422200 | Weak transcription | Breast variant Human Mammary Epithelial Cells (vHMEC) | Breast |
