Variant report
| Variant | rs2525543 |
|---|---|
| Chromosome Location | chr7:99548648-99548649 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:9)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:9 , 50 per page) page:
1
| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | CBX3 | chr7:99548473-99548806 | HCT-116 | colon: | n/a | n/a |
| 2 | TRIM28 | chr7:99548510-99548738 | K562 | blood: | n/a | n/a |
| 3 | SETDB1 | chr7:99548315-99548810 | U2OS | brain: | n/a | n/a |
| 4 | ZNF143 | chr7:99548462-99548734 | H1-hESC | embryonic stem cell: | n/a | n/a |
| 5 | KAP1 | chr7:99548296-99548904 | K562 | blood: | n/a | n/a |
| 6 | TRIM28 | chr7:99548356-99548837 | K562 | blood: | n/a | n/a |
| 7 | CBX3 | chr7:99548435-99548808 | K562 | blood: | n/a | n/a |
| 8 | CBX3 | chr7:99548459-99548786 | K562 | blood: | n/a | n/a |
| 9 | ZNF143 | chr7:99548535-99548676 | K562 | blood: | n/a | n/a |
| No data |
(count:1 , 50 per page) page:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr7:99546378..99548989-chr7:99551538..99554041,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000222966 | TF binding region |
rSNPs within LD-proxies of this variant (count:16)
| rs_ID | r2[population] |
|---|---|
| rs1981549 | 0.98[ASN][1000 genomes] |
| rs2040787 | 0.98[ASN][1000 genomes] |
| rs2404975 | 0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs2525535 | 0.98[ASN][1000 genomes] |
| rs2525536 | 0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs2525539 | 0.98[ASN][1000 genomes] |
| rs2525540 | 0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs2525545 | 0.96[ASN][1000 genomes] |
| rs2525549 | 0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs2525550 | 0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs2525558 | 0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs2527887 | 0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs2527888 | 0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs2527889 | 0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs2527898 | 0.97[ASN][1000 genomes] |
| rs35656988 | 0.96[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | esv1829865 | chr7:99430678-99755141 | Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 1131 gene(s) | inside rSNPs | diseases |
| 2 | esv1830649 | chr7:99430678-99755141 | Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 1131 gene(s) | inside rSNPs | diseases |
| 3 | nsv534298 | chr7:99478011-99886076 | Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 1132 gene(s) | inside rSNPs | diseases |
| 4 | nsv607930 | chr7:99525241-99602191 | Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 22 gene(s) | inside rSNPs | diseases |
| 5 | esv1828362 | chr7:99530233-99628773 | Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 39 gene(s) | inside rSNPs | diseases |
| 6 | nsv888772 | chr7:99533178-99602191 | Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 20 gene(s) | inside rSNPs | diseases |
| 7 | esv1830255 | chr7:99544908-99626331 | Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 38 gene(s) | inside rSNPs | diseases |
| 8 | esv1832985 | chr7:99546856-99615911 | Active TSS Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 38 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:3)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs2525543 | TRIM4 | cis | multi-tissue | Pritchard |
| rs2525543 | TRIM4 | Cis_1M | lymphoblastoid | RTeQTL |
| rs2525543 | TRIM4 | cis | Thyroid | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr7:99546400-99552800 | Weak transcription | Foreskin Melanocyte Primary Cells skin03 | Skin |
| 2 | chr7:99548000-99548800 | ZNF genes & repeats | ES-UCSF4 Cell Line | embryonic stem cell |
