Variant report
| Variant | rs11583927 |
|---|---|
| Chromosome Location | chr1:166850207-166850208 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:4)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:4 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr1:166849563..166852830-chr1:166854129..166856433,3 | K562 | blood: | |
| 2 | chr1:166843592..166845606-chr1:166849976..166852401,3 | MCF-7 | breast: | |
| 3 | chr1:166844292..166848543-chr1:166849353..166853640,5 | K562 | blood: | |
| 4 | chr1:166843731..166846321-chr1:166849999..166852051,3 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000152382 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:26)
| rs_ID | r2[population] |
|---|---|
| rs10800270 | 0.85[ASN][1000 genomes] |
| rs10800276 | 1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.98[ASN][1000 genomes] |
| rs11576904 | 0.88[CEU][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes] |
| rs11584352 | 1.00[ASN][1000 genomes] |
| rs12062326 | 0.80[ASN][1000 genomes] |
| rs12562794 | 0.91[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes] |
| rs1476347 | 0.82[CHB][hapmap] |
| rs1543313 | 0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs2038020 | 0.93[EUR][1000 genomes] |
| rs2038022 | 0.92[CEU][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes] |
| rs2072740 | 0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs2075946 | 0.82[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes] |
| rs2223221 | 0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs2280995 | 1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes] |
| rs2294195 | 0.95[ASN][1000 genomes] |
| rs2294220 | 0.83[EUR][1000 genomes] |
| rs34381372 | 0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs3820387 | 0.81[JPT][hapmap] |
| rs4656516 | 0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs4657609 | 0.98[ASN][1000 genomes] |
| rs4657612 | 0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs4657613 | 1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes] |
| rs6677644 | 0.89[TSI][hapmap] |
| rs7513457 | 0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs7520897 | 0.89[TSI][hapmap] |
| rs9633326 | 0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[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 | nsv916491 | chr1:166000783-166948513 | Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 38 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:3)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs11583927 | TBX19 | cis | cerebellum | SCAN |
| rs11583927 | TADA1 | cis | cerebellum | SCAN |
| rs11583927 | APOA2 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:166846200-166853200 | Weak transcription | Right Atrium | heart |
