Variant report
| Variant | rs4254394 |
|---|---|
| Chromosome Location | chr18:29539540-29539541 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:2)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:2 , 50 per page) page:
1
| No data |
(count:1 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr18:29523716..29526205-chr18:29536614..29539662,3 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| PGDP1 | TF binding region |
rSNPs within LD-proxies of this variant (count:18)
| rs_ID | r2[population] |
|---|---|
| rs1030403 | 0.92[ASN][1000 genomes] |
| rs12455103 | 0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs4239371 | 0.87[ASN][1000 genomes] |
| rs4799610 | 0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes] |
| rs4799611 | 0.92[ASN][1000 genomes] |
| rs4799612 | 0.89[ASN][1000 genomes] |
| rs4799614 | 0.92[ASN][1000 genomes] |
| rs67236500 | 0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs7244936 | 0.81[AMR][1000 genomes];0.92[ASN][1000 genomes] |
| rs7245194 | 0.87[ASN][1000 genomes] |
| rs8083160 | 0.91[ASN][1000 genomes] |
| rs8086309 | 0.94[ASN][1000 genomes] |
| rs8095233 | 0.92[ASN][1000 genomes] |
| rs8096737 | 0.92[ASN][1000 genomes] |
| rs8097869 | 0.92[ASN][1000 genomes] |
| rs8098106 | 0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes] |
| rs9676072 | 0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes] |
| rs972357 | 0.92[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 | nsv1067252 | chr18:29475073-29583744 | Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 17 gene(s) | inside rSNPs | diseases |
| 2 | nsv1065285 | chr18:29527884-29614986 | Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 12 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr18:29539400-29545200 | Weak transcription | Fetal Intestine Small | intestine |
