Variant report
| Variant | rs2485885 |
|---|---|
| Chromosome Location | chr1:210356013-210356014 |
| allele | C/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 | chr1:210350899..210352953-chr1:210354578..210356622,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:30)
| rs_ID | r2[population] |
|---|---|
| rs12401646 | 0.81[ASN][1000 genomes] |
| rs1338286 | 0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes] |
| rs1338298 | 1.00[YRI][hapmap] |
| rs17318612 | 0.81[ASN][1000 genomes] |
| rs17318744 | 0.81[ASN][1000 genomes] |
| rs1806963 | 0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes] |
| rs2096152 | 0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes] |
| rs2451696 | 0.92[ASN][1000 genomes] |
| rs2451697 | 0.92[ASN][1000 genomes] |
| rs2484030 | 0.95[ASN][1000 genomes] |
| rs2484031 | 0.95[ASN][1000 genomes] |
| rs2484032 | 1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes] |
| rs2484034 | 1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes] |
| rs2485883 | 0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes] |
| rs2485884 | 0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs2485897 | 0.86[AMR][1000 genomes];0.95[ASN][1000 genomes] |
| rs2485898 | 0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes] |
| rs2485902 | 0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes] |
| rs2487907 | 0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes] |
| rs2494170 | 0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs2494183 | 0.84[YRI][hapmap] |
| rs2494184 | 0.84[YRI][hapmap] |
| rs2494191 | 0.83[AMR][1000 genomes];0.92[ASN][1000 genomes] |
| rs35256257 | 0.81[ASN][1000 genomes] |
| rs35640054 | 0.81[AMR][1000 genomes];0.83[EUR][1000 genomes] |
| rs4844954 | 1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes] |
| rs61820397 | 0.81[ASN][1000 genomes] |
| rs61826848 | 0.81[ASN][1000 genomes] |
| rs6540578 | 0.81[ASN][1000 genomes] |
| rs654523 | 1.00[YRI][hapmap] |
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 | nsv1014034 | chr1:209759648-210501731 | Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 45 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs2485885 | G0S2 | cis | lymphoblastoid | seeQTL |
| rs2485885 | DIEXF | cis | lymphoblastoid | seeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:210339400-210361200 | Weak transcription | Breast variant Human Mammary Epithelial Cells (vHMEC) | Breast |
