Variant report
| Variant | rs10954040 |
|---|---|
| Chromosome Location | chr7:124209320-124209321 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:1)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
| No data |
(count:1 , 50 per page) page:
1
| No. | lncRNA name | Chromosome Location | lncRNA alias |
|---|---|---|---|
| 1 | lnc-GPR37-3 | chr7:124209293-124209366 | ucscGeneNc_uc003vlj_1 |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:14)
| rs_ID | r2[population] |
|---|---|
| rs10243704 | 0.86[EUR][1000 genomes] |
| rs1073554 | 0.87[EUR][1000 genomes] |
| rs1181796 | 0.89[EUR][1000 genomes] |
| rs12668485 | 0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs13239002 | 0.80[EUR][1000 genomes] |
| rs13239082 | 0.80[EUR][1000 genomes] |
| rs1568813 | 0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs17147231 | 0.93[EUR][1000 genomes] |
| rs17147238 | 0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs1917352 | 0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs1949834 | 0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs35936075 | 0.81[ASN][1000 genomes] |
| rs73219091 | 0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs7791861 | 0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv429809 | chr7:123937674-124835925 | Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 49 gene(s) | inside rSNPs | diseases |
| 2 | nsv831118 | chr7:124172267-124347527 | Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:4)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs10954040 | KCND2 | cis | parietal | SCAN |
| rs10954040 | TSPAN12 | cis | parietal | SCAN |
| rs10954040 | LMOD2 | cis | cerebellum | SCAN |
| rs10954040 | LOC154872 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr7:124208800-124209600 | Enhancers | Fetal Adrenal Gland | Adrenal Gland |
