Variant report
| Variant | rs10034779 |
|---|---|
| Chromosome Location | chr4:121860849-121860850 |
| allele | A/C |
| 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:21)
| rs_ID | r2[population] |
|---|---|
| rs11931234 | 0.85[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs11935242 | 0.85[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs11939905 | 0.85[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs11942376 | 0.85[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs11942389 | 0.85[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs1450476 | 0.83[GIH][hapmap] |
| rs17051270 | 1.00[ASW][hapmap];0.83[GIH][hapmap] |
| rs17051280 | 0.85[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs2278811 | 0.92[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs4833682 | 1.00[ASW][hapmap] |
| rs55930284 | 0.92[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs55962052 | 0.81[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs56004809 | 0.81[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs56270962 | 0.81[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs56339840 | 0.81[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs60983006 | 0.81[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs73843656 | 0.81[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs73843658 | 0.81[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs73843660 | 0.88[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs885460 | 0.85[CEU][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs9992516 | 0.88[AFR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv998094 | chr4:121504565-122374203 | Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 20 gene(s) | inside rSNPs | diseases |
| 2 | nsv1009395 | chr4:121841442-122557363 | Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 15 gene(s) | inside rSNPs | diseases |
| 3 | nsv537235 | chr4:121841442-122557363 | Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 15 gene(s) | inside rSNPs | diseases |
| 4 | esv3467361 | chr4:121856785-121861728 | Enhancers | n/a | n/a | inside rSNPs | diseases |
| 5 | esv3467362 | chr4:121856785-121861728 | Enhancers | n/a | n/a | inside rSNPs | diseases |
| 6 | nsv822713 | chr4:121856896-121861600 | Enhancers | n/a | n/a | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs10034779 | NDST3 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr4:121860800-121861200 | Enhancers | Breast variant Human Mammary Epithelial Cells (vHMEC) | Breast |
