Variant report
| Variant | rs2184065 |
|---|---|
| Chromosome Location | chr1:160940032-160940033 |
| 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 | chr1:160939974..160941495-chr1:160951029..160953259,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:30)
| rs_ID | r2[population] |
|---|---|
| rs10737178 | 0.85[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap] |
| rs12116949 | 1.00[LWK][hapmap] |
| rs2039223 | 1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap] |
| rs2245672 | 0.96[ASN][1000 genomes] |
| rs2246145 | 1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes] |
| rs2246484 | 0.96[ASN][1000 genomes] |
| rs2246485 | 0.96[ASN][1000 genomes] |
| rs2247472 | 1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap] |
| rs2249409 | 0.94[ASN][1000 genomes] |
| rs2249933 | 0.84[ASN][1000 genomes] |
| rs2250174 | 0.84[ASN][1000 genomes] |
| rs2250193 | 0.84[ASN][1000 genomes] |
| rs2250304 | 0.84[ASN][1000 genomes] |
| rs2256505 | 0.96[ASN][1000 genomes] |
| rs2256625 | 1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes] |
| rs2265239 | 0.85[ASN][1000 genomes] |
| rs2265240 | 0.94[ASN][1000 genomes] |
| rs2265242 | 0.87[ASN][1000 genomes] |
| rs2481073 | 0.96[ASN][1000 genomes] |
| rs2481076 | 0.84[EUR][1000 genomes] |
| rs2483139 | 1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes] |
| rs2483140 | 0.96[ASN][1000 genomes] |
| rs2483141 | 0.92[CHB][hapmap] |
| rs2779801 | 0.96[ASN][1000 genomes] |
| rs2990694 | 0.94[ASN][1000 genomes] |
| rs4483427 | 0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes] |
| rs6427563 | 0.96[ASN][1000 genomes] |
| rs6677533 | 0.99[ASN][1000 genomes] |
| rs790055 | 1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap] |
| rs790056 | 1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap] |
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 | nsv530077 | chr1:160836448-161284904 | Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 119 gene(s) | inside rSNPs | diseases |
| 2 | nsv548058 | chr1:160925455-160989614 | Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 19 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:5)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs2184065 | F11R | Cis_1M | lymphoblastoid | RTeQTL |
| rs2184065 | OR6K6 | cis | cerebellum | SCAN |
| rs2184065 | DEDD | cis | parietal | SCAN |
| rs2184065 | SLAMF8 | cis | parietal | SCAN |
| rs2184065 | OR6K3 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:160931000-160942000 | Weak transcription | H9 Cell Line | embryonic stem cell |
| 2 | chr1:160938000-160941200 | Weak transcription | iPS DF 19.11 Cell Line | embryonic stem cell |
| 3 | chr1:160939000-160941200 | Weak transcription | H1 Cell Line | embryonic stem cell |
