Variant report
| Variant | rs11197887 |
|---|---|
| Chromosome Location | chr10:118836682-118836683 |
| allele | A/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:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr10:118832679..118834580-chr10:118836577..118838384,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:27)
| rs_ID | r2[population] |
|---|---|
| rs10128516 | 0.92[CEU][hapmap];0.81[EUR][1000 genomes] |
| rs10749237 | 0.88[EUR][1000 genomes] |
| rs10787751 | 0.99[EUR][1000 genomes] |
| rs10886037 | 1.00[AMR][1000 genomes];0.99[EUR][1000 genomes] |
| rs10886038 | 0.92[CEU][hapmap];0.90[EUR][1000 genomes] |
| rs10886040 | 0.95[AMR][1000 genomes];0.97[EUR][1000 genomes] |
| rs11197892 | 1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs11197899 | 0.95[AMR][1000 genomes];0.96[EUR][1000 genomes] |
| rs12244454 | 0.82[EUR][1000 genomes] |
| rs12268087 | 0.88[EUR][1000 genomes] |
| rs1865954 | 0.90[EUR][1000 genomes] |
| rs1865955 | 0.90[EUR][1000 genomes] |
| rs1898349 | 0.81[AMR][1000 genomes];0.96[EUR][1000 genomes] |
| rs1898351 | 0.88[EUR][1000 genomes] |
| rs1898357 | 0.90[EUR][1000 genomes] |
| rs1947798 | 0.88[EUR][1000 genomes] |
| rs2420308 | 0.92[CEU][hapmap];0.90[EUR][1000 genomes] |
| rs3847479 | 0.92[CEU][hapmap];0.90[EUR][1000 genomes] |
| rs4752028 | 1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs7069235 | 0.84[AMR][1000 genomes];0.95[EUR][1000 genomes] |
| rs7072663 | 0.82[EUR][1000 genomes] |
| rs7078823 | 0.82[EUR][1000 genomes] |
| rs7085083 | 0.87[EUR][1000 genomes] |
| rs7087662 | 0.83[EUR][1000 genomes] |
| rs7093171 | 0.86[EUR][1000 genomes] |
| rs751232 | 0.82[EUR][1000 genomes] |
| rs7917897 | 0.87[EUR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv832002 | chr10:118797070-119005840 | Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA | 24 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:5)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs11197887 | KIAA1598 | cis | multi-tissue | Pritchard |
| rs11197887 | KIAA1598 | cis | Whole Blood | GTEx |
| rs11197887 | VWA2 | cis | cerebellum | SCAN |
| rs11197887 | DKFZp781N1041 | cis | multi-tissue | Pritchard |
| rs11197887 | GFRA1 | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr10:118834800-118837600 | Weak transcription | A549 | lung |
| 2 | chr10:118835000-118837800 | Weak transcription | Breast variant Human Mammary Epithelial Cells (vHMEC) | Breast |
