Variant report
| Variant | rs17277372 |
|---|---|
| Chromosome Location | chr1:172187474-172187475 |
| allele | A/G |
| 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:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr1:172182635..172185349-chr1:172186407..172188943,2 | K562 | blood: |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:12)
| rs_ID | r2[population] |
|---|---|
| rs10489293 | 1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes] |
| rs10489297 | 0.91[GIH][hapmap];0.90[TSI][hapmap] |
| rs11589142 | 0.88[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes] |
| rs16844417 | 1.00[CHD][hapmap] |
| rs17278379 | 1.00[CHD][hapmap] |
| rs17361886 | 0.88[GIH][hapmap];0.90[TSI][hapmap] |
| rs2209096 | 0.88[GIH][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap] |
| rs2421990 | 0.88[GIH][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes] |
| rs2421991 | 0.88[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes] |
| rs55935473 | 0.81[EUR][1000 genomes] |
| rs593688 | 0.88[GIH][hapmap];0.90[TSI][hapmap] |
| rs7535241 | 0.81[EUR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1000079 | chr1:172146935-172230545 | Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription | Chromatin interactive region | 1 gene(s) | inside rSNPs | diseases |
| 2 | nsv465650 | chr1:172175115-172247127 | Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription | Chromatin interactive regionlncRNA | 1 gene(s) | inside rSNPs | diseases |
| 3 | nsv548192 | chr1:172175115-172247127 | Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats | Chromatin interactive regionlncRNA | 1 gene(s) | inside rSNPs | diseases |
| 4 | nsv872546 | chr1:172186321-172219995 | Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS | Chromatin interactive region | n/a | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs17277372 | CREG1 | cis | cerebellum | SCAN |
| rs17277372 | FMO1 | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:172176600-172189800 | Weak transcription | Breast variant Human Mammary Epithelial Cells (vHMEC) | Breast |
