Variant report
| Variant | rs1378659 |
|---|---|
| Chromosome Location | chr3:160406325-160406326 |
| 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 | chr3:160406185..160409170-chr3:160413617..160415924,2 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000207084 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:20)
| rs_ID | r2[population] |
|---|---|
| rs10433459 | 1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs11707740 | 0.89[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes] |
| rs12638557 | 0.90[AMR][1000 genomes];0.87[EUR][1000 genomes] |
| rs13062999 | 0.91[AMR][1000 genomes];0.85[EUR][1000 genomes] |
| rs13092981 | 0.90[AMR][1000 genomes];0.85[EUR][1000 genomes] |
| rs1378661 | 0.90[AMR][1000 genomes];0.87[EUR][1000 genomes] |
| rs1455872 | 0.89[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs16831361 | 0.89[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs17217147 | 0.82[AMR][1000 genomes];0.91[EUR][1000 genomes] |
| rs2366967 | 0.90[AMR][1000 genomes];0.87[EUR][1000 genomes] |
| rs34275580 | 0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs35355599 | 0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes] |
| rs7633816 | 0.85[CEU][hapmap] |
| rs7649322 | 0.82[EUR][1000 genomes] |
| rs7651855 | 1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap] |
| rs7651941 | 1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs959826 | 0.90[AMR][1000 genomes];0.85[EUR][1000 genomes] |
| rs9820796 | 0.89[CEU][hapmap];0.81[EUR][1000 genomes] |
| rs9835634 | 0.89[CEU][hapmap];0.81[EUR][1000 genomes] |
| rs994966 | 0.81[EUR][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 | nsv532666 | chr3:159777847-160703202 | Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 271 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:3)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs1378659 | IFT80 | cis | parietal | SCAN |
| rs1378659 | ARL14 | cis | cerebellum | SCAN |
| rs1378659 | PPM1L | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr3:160397000-160412800 | Weak transcription | H1 BMP4 Derived Trophoblast Cultured Cells | ES cell derived |
| 2 | chr3:160404800-160407000 | Enhancers | Hela-S3 | cervix |
