Variant report
| Variant | rs27628 |
|---|---|
| Chromosome Location | chr5:50230371-50230372 |
| allele | G/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:2)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:2 , 50 per page) page:
1
| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | SPI1 | chr5:50230195-50230610 | HL-60 | blood: | n/a | chr5:50230360-50230373 |
| 2 | SPI1 | chr5:50230258-50230455 | K562 | blood: | n/a | chr5:50230360-50230373 |
| No data |
| No data |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000251601 | TF binding region |
rSNPs within LD-proxies of this variant (count:10)
| rs_ID | r2[population] |
|---|---|
| rs151997 | 0.82[JPT][hapmap] |
| rs152699 | 1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs152700 | 0.90[AFR][1000 genomes];0.88[ASN][1000 genomes] |
| rs152817 | 0.82[JPT][hapmap] |
| rs152819 | 0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs27247 | 0.82[JPT][hapmap] |
| rs27248 | 1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs27249 | 0.82[JPT][hapmap] |
| rs3846499 | 0.82[JPT][hapmap] |
| rs3846500 | 0.82[JPT][hapmap] |
Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1034445 | chr5:49986171-50492609 | Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 16 gene(s) | inside rSNPs | diseases |
| 2 | nsv598116 | chr5:50064292-50318550 | Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 11 gene(s) | inside rSNPs | diseases |
| 3 | nsv830286 | chr5:50165805-50374600 | Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 10 gene(s) | inside rSNPs | diseases |
| 4 | nsv1034194 | chr5:50209649-50234259 | Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive region | 1 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs27628 | TMCC3 | trans | parietal | SCAN |
| rs27628 | SRSF5 | trans | parietal | SCAN |
Chromatin state (count:0 , 50 per page) page:
| No data |
