Variant report
| Variant | rs12471663 |
|---|---|
| Chromosome Location | chr2:190507098-190507099 |
| 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 | chr2:190505910..190508491-chr2:190509501..190513680,4 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:20)
| rs_ID | r2[population] |
|---|---|
| rs10931430 | 0.81[ASN][1000 genomes] |
| rs11679767 | 0.81[ASN][1000 genomes] |
| rs12693551 | 0.83[AFR][1000 genomes];0.83[ASN][1000 genomes] |
| rs2289226 | 0.86[AFR][1000 genomes] |
| rs4667295 | 0.82[AMR][1000 genomes] |
| rs4667296 | 0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs4667297 | 0.89[AFR][1000 genomes];0.83[ASN][1000 genomes] |
| rs4667299 | 0.81[ASN][1000 genomes] |
| rs61487110 | 0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes] |
| rs6434355 | 0.80[AMR][1000 genomes];0.83[EUR][1000 genomes] |
| rs6434361 | 0.83[AFR][1000 genomes];0.80[ASN][1000 genomes] |
| rs6756040 | 0.83[EUR][1000 genomes] |
| rs6756571 | 0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs6756657 | 0.83[EUR][1000 genomes] |
| rs6756913 | 0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs6761923 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs7568449 | 0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes] |
| rs7577644 | 0.83[EUR][1000 genomes] |
| rs893784 | 0.82[ASN][1000 genomes] |
| rs9646811 | 0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][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 | nsv533029 | chr2:189812229-190554339 | Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 40 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:6)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs12471663 | ASNSD1 | Cis_1M | lymphoblastoid | RTeQTL |
| rs12471663 | PMS1 | Cis_1M | lymphoblastoid | RTeQTL |
| rs12471663 | ORMDL1 | Cis_1M | lymphoblastoid | RTeQTL |
| rs12471663 | ORMDL1 | cis | Adipose Subcutaneous | GTEx |
| rs12471663 | ORMDL1 | cis | Skin Sun Exposed Lower leg | GTEx |
| rs12471663 | ASNSD1 | cis | Whole Blood | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr2:190506800-190522400 | Weak transcription | H1 BMP4 Derived Mesendoderm Cultured Cells | ES cell derived |
| 2 | chr2:190507000-190508000 | Enhancers | Fetal Intestine Small | intestine |
