Variant report
| Variant | rs4602859 |
|---|---|
| Chromosome Location | chr8:105481352-105481353 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:5)
- CpG islands (count:0)
- Chromatin interactive region (count:2)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:5 , 50 per page) page:
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| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | YY1 | chr8:105481149-105481649 | K562 | blood: | n/a | chr8:105481473-105481485 chr8:105481495-105481507 |
| 2 | BHLHE40 | chr8:105481322-105481496 | K562 | blood: | n/a | n/a |
| 3 | YY1 | chr8:105481334-105481601 | H1-hESC | embryonic stem cell: | n/a | chr8:105481473-105481485 chr8:105481495-105481507 |
| 4 | YY1 | chr8:105481258-105481672 | H1-hESC | embryonic stem cell: | n/a | chr8:105481473-105481485 chr8:105481495-105481507 |
| 5 | YY1 | chr8:105481125-105481634 | K562 | blood: | n/a | chr8:105481473-105481485 chr8:105481495-105481507 |
| No data |
(count:2 , 50 per page) page:
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| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| DPYS | TF binding region |
rSNPs within LD-proxies of this variant (count:14)
| rs_ID | r2[population] |
|---|---|
| rs12543329 | 0.88[ASN][1000 genomes] |
| rs12546843 | 0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs12550349 | 0.87[ASN][1000 genomes] |
| rs12680920 | 0.80[ASN][1000 genomes] |
| rs2298840 | 0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs3750187 | 0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs4474003 | 0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs62510142 | 0.80[ASN][1000 genomes] |
| rs66479713 | 0.85[AMR][1000 genomes];0.90[ASN][1000 genomes] |
| rs67403507 | 0.81[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs72679133 | 0.81[EUR][1000 genomes] |
| rs72679139 | 0.81[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs73293244 | 0.83[ASN][1000 genomes] |
| rs73295140 | 0.87[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page:
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| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1016087 | chr8:105228670-105934368 | Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 21 gene(s) | inside rSNPs | diseases |
| 2 | nsv1026754 | chr8:105382508-106030916 | Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA | 18 gene(s) | inside rSNPs | diseases |
| 3 | nsv539709 | chr8:105382508-106030916 | Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA | 18 gene(s) | inside rSNPs | diseases |
| 4 | nsv831417 | chr8:105455814-105625608 | Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA | 7 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs4602859 | LRP12 | cis | Skin Sun Exposed Lower leg | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr8:105480600-105483600 | Weak transcription | Liver | Liver |
