Variant report
| Variant | rs12331454 |
|---|---|
| Chromosome Location | chr4:119504371-119504372 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:1 , 50 per page) page:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr4:119503145..119504877-chr4:119508741..119511511,2 | K562 | blood: |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:22)
| rs_ID | r2[population] |
|---|---|
| rs10004322 | 0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs10022024 | 0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs10031029 | 0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes] |
| rs10857060 | 0.97[ASN][1000 genomes] |
| rs11728902 | 0.83[EUR][1000 genomes] |
| rs11734153 | 0.97[ASN][1000 genomes] |
| rs13137401 | 0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs2389780 | 0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs2728403 | 0.84[EUR][1000 genomes] |
| rs2787191 | 0.88[EUR][1000 genomes] |
| rs28448851 | 0.85[AMR][1000 genomes];0.94[EUR][1000 genomes] |
| rs35890030 | 0.95[ASN][1000 genomes] |
| rs4001330 | 0.84[ASN][1000 genomes] |
| rs67276048 | 0.82[EUR][1000 genomes] |
| rs67655207 | 0.81[EUR][1000 genomes] |
| rs71241793 | 0.80[EUR][1000 genomes] |
| rs71610209 | 0.84[ASN][1000 genomes] |
| rs72676188 | 0.92[ASN][1000 genomes] |
| rs7656990 | 0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs7669896 | 0.97[ASN][1000 genomes] |
| rs7689541 | 0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs9760578 | 0.81[EUR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv519017 | chr4:118828807-119771481 | Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 39 gene(s) | inside rSNPs | diseases |
| 2 | nsv1002771 | chr4:119125361-119571237 | Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 28 gene(s) | inside rSNPs | diseases |
| 3 | nsv1003731 | chr4:119138262-119506032 | Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 22 gene(s) | inside rSNPs | diseases |
| 4 | esv3355840 | chr4:119296640-119774737 | Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 20 gene(s) | inside rSNPs | diseases |
| 5 | nsv427693 | chr4:119493919-119674742 | Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 16 gene(s) | inside rSNPs | diseases |
| 6 | nsv967680 | chr4:119499004-119506088 | Enhancers Bivalent Enhancer Active TSS Weak transcription | Chromatin interactive region | n/a | inside rSNPs | diseases |
| 7 | nsv980150 | chr4:119499004-119514502 | Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive region | 1 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:16)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs12331454 | RP11-384K6.2 | cis | Whole Blood | GTEx |
| rs12331454 | RP11-384K6.6 | cis | Esophagus Muscularis | GTEx |
| rs12331454 | RP11-384K6.2 | cis | lung | GTEx |
| rs12331454 | RP11-384K6.2 | cis | Artery Tibial | GTEx |
| rs12331454 | RP11-384K6.6 | cis | Whole Blood | GTEx |
| rs12331454 | RP11-384K6.2 | cis | Skin Sun Exposed Lower leg | GTEx |
| rs12331454 | RP11-384K6.6 | cis | Artery Tibial | GTEx |
| rs12331454 | RP11-384K6.6 | cis | Adipose Subcutaneous | GTEx |
| rs12331454 | RP11-384K6.6 | cis | Esophagus Mucosa | GTEx |
| rs12331454 | RP11-384K6.6 | cis | Thyroid | GTEx |
| rs12331454 | RP11-384K6.2 | cis | Nerve Tibial | GTEx |
| rs12331454 | RP11-384K6.6 | cis | Skin Sun Exposed Lower leg | GTEx |
| rs12331454 | RP11-384K6.2 | cis | Thyroid | GTEx |
| rs12331454 | RP11-384K6.2 | cis | Adipose Subcutaneous | GTEx |
| rs12331454 | RP11-384K6.6 | cis | lung | GTEx |
| rs12331454 | RP11-384K6.6 | cis | Nerve Tibial | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr4:119504000-119507000 | Weak transcription | H1 BMP4 Derived Mesendoderm Cultured Cells | ES cell derived |
