Variant report
| Variant | rs7308874 |
|---|---|
| Chromosome Location | chr12:42027870-42027871 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
| No data |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:25)
| rs_ID | r2[population] |
|---|---|
| rs10506196 | 1.00[GIH][hapmap] |
| rs11181005 | 1.00[GIH][hapmap];1.00[TSI][hapmap] |
| rs12227540 | 1.00[GIH][hapmap] |
| rs12581662 | 0.80[ASN][1000 genomes] |
| rs17129591 | 0.98[ASN][1000 genomes] |
| rs17129603 | 0.98[ASN][1000 genomes] |
| rs185937 | 0.98[ASN][1000 genomes] |
| rs286977 | 0.98[ASN][1000 genomes] |
| rs286995 | 0.98[ASN][1000 genomes] |
| rs287034 | 0.98[ASN][1000 genomes] |
| rs287035 | 0.89[ASN][1000 genomes] |
| rs287036 | 0.98[ASN][1000 genomes] |
| rs287038 | 0.93[ASN][1000 genomes] |
| rs287041 | 0.98[ASN][1000 genomes] |
| rs287046 | 0.98[ASN][1000 genomes] |
| rs287047 | 0.98[ASN][1000 genomes] |
| rs287049 | 0.98[ASN][1000 genomes] |
| rs287051 | 0.98[ASN][1000 genomes] |
| rs407628 | 0.98[ASN][1000 genomes] |
| rs426443 | 0.98[ASN][1000 genomes] |
| rs59284651 | 0.98[ASN][1000 genomes] |
| rs60761629 | 0.97[ASN][1000 genomes] |
| rs7310375 | 0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs74078248 | 0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes] |
| rs754143 | 0.98[ASN][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 | esv3337301 | chr12:41851654-42093677 | Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
| 2 | nsv899040 | chr12:41905897-42181706 | Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
| 3 | nsv899041 | chr12:42005690-42072514 | Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS | TF binding regionCpG islandChromatin interactive region | 1 gene(s) | inside rSNPs | diseases |
| 4 | nsv832386 | chr12:42017259-42189476 | Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs7308874 | SMAD5 | trans | brain | seeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr12:42024200-42029400 | Weak transcription | Fetal Brain Male | brain |
