Variant report
| Variant | rs412878 |
|---|---|
| Chromosome Location | chr1:213729352-213729353 |
| allele | A/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 | chr1:213729027..213731700-chr1:214452978..214455881,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000143499 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:25)
| rs_ID | r2[population] |
|---|---|
| rs10864052 | 0.94[EUR][1000 genomes] |
| rs12021535 | 0.82[ASN][1000 genomes] |
| rs12023183 | 0.82[ASN][1000 genomes] |
| rs12026459 | 0.82[ASN][1000 genomes] |
| rs12026491 | 0.82[ASN][1000 genomes] |
| rs12029131 | 0.91[EUR][1000 genomes] |
| rs12033788 | 0.82[ASN][1000 genomes] |
| rs1371291 | 0.94[EUR][1000 genomes] |
| rs2218115 | 0.93[EUR][1000 genomes] |
| rs320391 | 0.95[EUR][1000 genomes] |
| rs320392 | 0.95[EUR][1000 genomes] |
| rs400857 | 1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs4072954 | 0.94[EUR][1000 genomes] |
| rs410108 | 0.82[YRI][hapmap] |
| rs420627 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs4297263 | 0.93[EUR][1000 genomes] |
| rs436112 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs4475718 | 0.82[ASN][1000 genomes] |
| rs4655298 | 0.94[EUR][1000 genomes] |
| rs4655299 | 0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs55816435 | 0.82[ASN][1000 genomes] |
| rs56254675 | 0.82[ASN][1000 genomes] |
| rs56352066 | 0.82[ASN][1000 genomes] |
| rs6540792 | 0.93[EUR][1000 genomes] |
| rs7545069 | 0.96[EUR][1000 genomes] |
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 | nsv832525 | chr1:213580476-213782815 | Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
| 2 | esv3345878 | chr1:213714352-213841547 | Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | diseases |
| 3 | esv3426755 | chr1:213714443-213841514 | Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | diseases |
| 4 | esv3378592 | chr1:213714463-213841484 | Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs412878 | NCRNA00161 | trans | cerebellum | SCAN |
| rs412878 | PPP1R1C | trans | parietal | SCAN |
Chromatin state (count:0 , 50 per page) page:
| No data |
