Variant report
| Variant | rs860413 |
|---|---|
| Chromosome Location | chr5:35943042-35943043 |
| allele | G/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:17)
| rs_ID | r2[population] |
|---|---|
| rs10040617 | 0.94[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes] |
| rs10072204 | 0.90[AMR][1000 genomes];0.89[EUR][1000 genomes] |
| rs10472993 | 0.89[AMR][1000 genomes];0.89[EUR][1000 genomes] |
| rs11742240 | 0.83[MEX][hapmap] |
| rs12153578 | 0.87[YRI][hapmap] |
| rs17313508 | 1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes] |
| rs1993879 | 1.00[CEU][hapmap];0.82[GIH][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes] |
| rs4424017 | 0.90[AMR][1000 genomes];0.89[EUR][1000 genomes] |
| rs62352020 | 0.90[AMR][1000 genomes];0.90[EUR][1000 genomes] |
| rs6881706 | 0.83[MEX][hapmap] |
| rs6895627 | 0.90[AMR][1000 genomes];0.86[EUR][1000 genomes] |
| rs6897932 | 0.89[ASW][hapmap];0.89[MEX][hapmap] |
| rs696734 | 0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes] |
| rs700172 | 1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap] |
| rs7717955 | 0.83[MEX][hapmap];0.87[YRI][hapmap] |
| rs7727279 | 0.87[AMR][1000 genomes];0.89[EUR][1000 genomes] |
| rs860412 | 0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes] |
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 | nsv471011 | chr5:35861068-36003217 | Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 8 gene(s) | inside rSNPs | diseases |
| 2 | nsv830261 | chr5:35863084-36018048 | Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 8 gene(s) | inside rSNPs | diseases |
| 3 | nsv1025695 | chr5:35902486-36036934 | Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 7 gene(s) | inside rSNPs | diseases |
Variant related diseases (count:1)
| Disease | PMID | Source |
|---|---|---|
| Primary biliary cirrhosis | 21399635 | GWAS catalog |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs860413 | SGK196 | trans | cerebellum | SCAN |
| rs860413 | C5orf33 | cis | cerebellum | SCAN |
Chromatin state (count:0 , 50 per page) page:
| No data |
