Variant report
| Variant | rs7408605 |
|---|---|
| Chromosome Location | chr19:42337718-42337719 |
| 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 | chr19:42337138..42340110-chr19:42342013..42344959,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000183103 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:4)
| rs_ID | r2[population] |
|---|---|
| rs1195088 | 0.97[ASN][1000 genomes] |
| rs1457143 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs2290695 | 0.80[MKK][hapmap] |
| rs2305809 | 0.80[MKK][hapmap] |
Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv522854 | chr19:42120283-42931004 | Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 104 gene(s) | inside rSNPs | diseases |
| 2 | nsv960847 | chr19:42319253-42339596 | Enhancers Bivalent Enhancer Weak transcription Genic enhancers | TF binding regionChromatin interactive regionlncRNA | 5 gene(s) | inside rSNPs | diseases |
| 3 | nsv1061878 | chr19:42325490-42416056 | Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 31 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:5)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs7408605 | CEACAM16 | cis | parietal | SCAN |
| rs7408605 | ZNF575 | cis | parietal | SCAN |
| rs7408605 | C19orf63 | cis | cerebellum | SCAN |
| rs7408605 | ZNF473 | cis | cerebellum | SCAN |
| rs7408605 | CEACAM1 | cis | cerebellum | SCAN |
Chromatin state (count:0 , 50 per page) page:
| No data |
