Variant report
| Variant | rs548333 |
|---|---|
| Chromosome Location | chr11:64197080-64197081 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:5)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:5 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr11:64189227..64191285-chr11:64196358..64198269,2 | K562 | blood: | |
| 2 | 11:64196069-64197420..11:64402707-64415880 | Hela-S3 | cervix: | |
| 3 | chr11:64196077..64197933-chr11:64215351..64217656,2 | MCF-7 | breast: | |
| 4 | 11:64196069-64197420..11:64415880-64426617 | Hela-S3 | cervix: | |
| 5 | 11:64196069-64197420..11:64501239-64517861 | Hela-S3 | cervix: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000068976 | Chromatin interaction |
| ENSG00000068831 | Chromatin interaction |
| ENSG00000181908 | Chromatin interaction |
| ENSG00000237410 | Chromatin interaction |
| ENSG00000110076 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:21)
| rs_ID | r2[population] |
|---|---|
| rs10792432 | 0.88[EUR][1000 genomes] |
| rs10897503 | 1.00[CEU][hapmap];0.96[EUR][1000 genomes] |
| rs12362958 | 0.87[AMR][1000 genomes];0.84[EUR][1000 genomes] |
| rs1662189 | 0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes] |
| rs28680814 | 0.87[AMR][1000 genomes];0.91[EUR][1000 genomes] |
| rs4930353 | 0.86[CEU][hapmap];0.92[CHB][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes] |
| rs521319 | 0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes] |
| rs550840 | 0.81[GIH][hapmap] |
| rs561667 | 0.83[EUR][1000 genomes] |
| rs562560 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs564163 | 0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes] |
| rs566409 | 0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes] |
| rs577304 | 0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes] |
| rs61884054 | 0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes] |
| rs653565 | 0.82[CEU][hapmap];0.92[CHB][hapmap];0.80[CHD][hapmap];0.92[GIH][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes] |
| rs653578 | 0.82[CEU][hapmap];0.92[CHB][hapmap];0.80[CHD][hapmap];0.92[GIH][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes] |
| rs72929971 | 1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes] |
| rs7936543 | 0.85[EUR][1000 genomes] |
| rs7937023 | 0.85[EUR][1000 genomes] |
| rs7937125 | 0.85[EUR][1000 genomes] |
| rs7951702 | 0.84[EUR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv832187 | chr11:64121969-64312300 | Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 50 gene(s) | inside rSNPs | diseases |
| 2 | nsv976458 | chr11:64183936-64198230 | Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 13 gene(s) | inside rSNPs | diseases |
| 3 | nsv976459 | chr11:64183936-64208134 | Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 13 gene(s) | inside rSNPs | diseases |
| 4 | nsv555194 | chr11:64189110-64238023 | Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 16 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:5)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs548333 | C11orf34 | trans | parietal | SCAN |
| rs548333 | MALAT1 | cis | cerebellum | SCAN |
| rs548333 | RBM14 | cis | parietal | SCAN |
| rs548333 | TMEM109 | cis | cerebellum | SCAN |
| rs548333 | DRAP1 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr11:64196400-64197200 | Enhancers | Fetal Brain Male | brain |
| 2 | chr11:64196400-64197600 | Weak transcription | hESC Derived CD56+ Ectoderm Cultured Cells | ES cell derived |
| 3 | chr11:64196800-64197800 | Bivalent Enhancer | Fetal Muscle Trunk | muscle |
| 4 | chr11:64197000-64198000 | Weak transcription | H1 Derived Neuronal Progenitor Cultured Cells | ES cell derived |
