Variant report
| Variant | rs857940 |
|---|---|
| Chromosome Location | chr1:158656973-158656974 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:9)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:9 , 50 per page) page:
1
| No data |
(count:1 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr1:158656464..158659384-chr1:159045094..159048407,3 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| SPTA1 | TF binding region |
| ENSG00000163568 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:17)
| rs_ID | r2[population] |
|---|---|
| rs2427804 | 0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs2518493 | 0.81[CHD][hapmap];0.88[JPT][hapmap] |
| rs28568406 | 0.86[EUR][1000 genomes] |
| rs399848 | 0.84[CEU][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes] |
| rs703118 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs703127 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs703134 | 0.96[EUR][1000 genomes] |
| rs703143 | 0.84[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes] |
| rs703144 | 0.84[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes] |
| rs751258 | 1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap] |
| rs857691 | 0.81[CHD][hapmap];0.88[JPT][hapmap] |
| rs857703 | 0.88[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes] |
| rs857925 | 0.84[CEU][hapmap] |
| rs857938 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs861409 | 0.88[JPT][hapmap] |
| rs863327 | 0.81[CHD][hapmap];0.88[JPT][hapmap] |
| rs864149 | 0.81[EUR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | esv3491788 | chr1:158537183-158725907 | Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 13 gene(s) | inside rSNPs | diseases |
| 2 | esv3491789 | chr1:158537242-158725858 | Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 13 gene(s) | inside rSNPs | diseases |
| 3 | nsv872481 | chr1:158625789-158712510 | Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Active TSS | TF binding regionCpG islandChromatin interactive region | 9 gene(s) | inside rSNPs | diseases |
| 4 | nsv872482 | chr1:158635852-158698532 | Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive region | 7 gene(s) | inside rSNPs | diseases |
| 5 | nsv872483 | chr1:158635852-158712510 | Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive region | 9 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:7)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs857940 | SCAMP3 | cis | parietal | SCAN |
| rs857940 | IQGAP3 | cis | cerebellum | SCAN |
| rs857940 | HCN3 | cis | cerebellum | SCAN |
| rs857940 | NCSTN | cis | parietal | SCAN |
| rs857940 | KIRREL | cis | cerebellum | SCAN |
| rs857940 | EFNA3 | cis | parietal | SCAN |
| rs857940 | S100A7A | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:158655200-158657000 | Active TSS | K562 | blood |
| 2 | chr1:158655800-158657000 | Enhancers | Primary hematopoietic stem cells G-CSF-mobilized Female | -- |
| 3 | chr1:158656200-158657000 | Enhancers | Monocytes-CD14+_RO01746 | blood |
| 4 | chr1:158656400-158657200 | Enhancers | Primary hematopoietic stem cells short term culture | blood |
