Variant report
| Variant | rs16832254 |
|---|---|
| Chromosome Location | chr2:190889261-190889262 |
| 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 | chr2:190888760..190889590-chr2:190934656..190935555,3 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:14)
| rs_ID | r2[population] |
|---|---|
| rs1036375 | 1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs1036376 | 0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs10931436 | 0.86[AFR][1000 genomes];0.81[AMR][1000 genomes] |
| rs10931437 | 0.86[AFR][1000 genomes];0.81[AMR][1000 genomes] |
| rs11694671 | 0.81[CEU][hapmap] |
| rs11900530 | 0.85[AMR][1000 genomes];0.82[ASN][1000 genomes] |
| rs12693559 | 0.85[AFR][1000 genomes];0.84[AMR][1000 genomes] |
| rs1474359 | 0.82[CEU][hapmap];0.93[GIH][hapmap] |
| rs2168058 | 0.87[AFR][1000 genomes];0.81[AMR][1000 genomes] |
| rs34806740 | 0.83[EUR][1000 genomes] |
| rs6760285 | 0.82[ASN][1000 genomes] |
| rs6761221 | 0.81[CEU][hapmap];0.91[GIH][hapmap] |
| rs72907398 | 0.82[ASN][1000 genomes] |
| rs72907401 | 0.82[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | esv3439094 | chr2:190852495-190889473 | ZNF genes & repeats Enhancers Weak transcription | Chromatin interactive region | n/a | inside rSNPs | diseases |
| 2 | esv3439178 | chr2:190877215-191124499 | Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 10 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:6)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs16832254 | PMS1 | cis | parietal | SCAN |
| rs16832254 | PMS1 | Cis_1M | lymphoblastoid | RTeQTL |
| rs16832254 | ORMDL1 | cis | multi-tissue | Pritchard |
| rs16832254 | PMS1 | cis | cerebellum | SCAN |
| rs16832254 | ORMDL1 | Cis_1M | lymphoblastoid | RTeQTL |
| rs16832254 | ASNSD1 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr2:190884400-190893000 | Weak transcription | H1 BMP4 Derived Mesendoderm Cultured Cells | ES cell derived |
