Variant report
| Variant | rs461488 |
|---|---|
| Chromosome Location | chr21:40025249-40025250 |
| allele | C/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 | chr21:40024195..40027388-chr21:40030048..40033604,4 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000157554 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:26)
| rs_ID | r2[population] |
|---|---|
| rs1015069 | 1.00[CEU][hapmap];0.98[EUR][1000 genomes] |
| rs1015070 | 1.00[CEU][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes] |
| rs1540015 | 0.81[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs1540016 | 1.00[CEU][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes] |
| rs2836600 | 0.96[YRI][hapmap] |
| rs2836613 | 0.91[EUR][1000 genomes] |
| rs2836619 | 0.88[EUR][1000 genomes] |
| rs2836620 | 0.80[EUR][1000 genomes] |
| rs458783 | 0.96[EUR][1000 genomes] |
| rs459813 | 0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs460112 | 1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes] |
| rs460843 | 0.90[CEU][hapmap];0.95[EUR][1000 genomes] |
| rs460947 | 0.96[EUR][1000 genomes] |
| rs461592 | 1.00[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes] |
| rs463269 | 0.95[CEU][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes] |
| rs463501 | 1.00[CEU][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes] |
| rs463530 | 0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes] |
| rs464519 | 0.86[JPT][hapmap] |
| rs465004 | 0.97[EUR][1000 genomes] |
| rs465327 | 0.81[AMR][1000 genomes];0.97[EUR][1000 genomes] |
| rs62217514 | 0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs8132920 | 0.95[CEU][hapmap];0.90[EUR][1000 genomes] |
| rs8134664 | 1.00[CEU][hapmap];0.98[EUR][1000 genomes] |
| rs9647180 | 0.98[EUR][1000 genomes] |
| rs994003 | 0.96[EUR][1000 genomes] |
| rs9975531 | 0.97[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 | nsv1057719 | chr21:40009959-40025433 | Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers | Chromatin interactive regionlncRNA | 1 gene(s) | inside rSNPs | diseases |
| 2 | nsv1058663 | chr21:40009959-40031681 | Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers | Chromatin interactive regionlncRNA | 1 gene(s) | inside rSNPs | diseases |
| 3 | nsv1055287 | chr21:40013735-40031681 | Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS | Chromatin interactive regionlncRNA | 1 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:4)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs461488 | HLCS | cis | parietal | SCAN |
| rs461488 | SETD4 | cis | parietal | SCAN |
| rs461488 | NCRNA00257 | cis | cerebellum | SCAN |
| rs461488 | RUNX1 | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr21:40016000-40027000 | Weak transcription | Primary hematopoietic stem cells G-CSF-mobilized Male | -- |
| 2 | chr21:40024000-40025400 | Genic enhancers | Breast Myoepithelial Primary Cells | Breast |
| 3 | chr21:40024800-40027400 | Weak transcription | Aorta | Aorta |
