Variant report
| Variant | rs11879355 |
|---|---|
| Chromosome Location | chr19:44306482-44306483 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:24)
- CpG islands (count:0)
- Chromatin interactive region (count:2)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:24 , 50 per page) page:
1
| No data |
(count:2 , 50 per page) page:
1
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| LYPD5 | TF binding region |
| ENSG00000159871 | Chromatin interaction |
| ENSG00000104783 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:10)
| rs_ID | r2[population] |
|---|---|
| rs11666403 | 0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs3786956 | 0.85[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.92[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap] |
| rs62116989 | 0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes] |
| rs62116993 | 0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs62116994 | 0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs62116995 | 0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs62116996 | 0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs62116997 | 0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs62116998 | 0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs8112656 | 1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv532821 | chr19:43842383-44357315 | Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 62 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:9)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs11879355 | SIGLEC11 | cis | parietal | SCAN |
| rs11879355 | ZNF649 | cis | parietal | SCAN |
| rs11879355 | ZNF610 | cis | parietal | SCAN |
| rs11879355 | IGFL2 | cis | parietal | SCAN |
| rs11879355 | ZNF615 | cis | parietal | SCAN |
| rs11879355 | KLK5 | cis | parietal | SCAN |
| rs11879355 | PRKD2 | cis | parietal | SCAN |
| rs11879355 | DHX34 | cis | parietal | SCAN |
| rs11879355 | KLK9 | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr19:44304200-44308600 | Weak transcription | K562 | blood |
| 2 | chr19:44304600-44309000 | Weak transcription | Spleen | Spleen |
| 3 | chr19:44304600-44310200 | Weak transcription | HMEC | breast |
| 4 | chr19:44304600-44310200 | Weak transcription | NHEK | skin |
