Variant report
| Variant | rs10749205 |
|---|---|
| Chromosome Location | chr10:118046389-118046390 |
| 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 | chr10:118041442..118043123-chr10:118044794..118046648,2 | K562 | blood: | |
| 2 | chr10:118035598..118037239-chr10:118045691..118047252,2 | MCF-7 | breast: | |
| 3 | chr10:118041451..118043258-chr10:118046041..118048376,2 | MCF-7 | breast: | |
| 4 | chr10:118030488..118032578-chr10:118042557..118047503,4 | MCF-7 | breast: | |
| 5 | chr10:118029653..118031249-chr10:118045197..118046929,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000151892 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:10)
| rs_ID | r2[population] |
|---|---|
| rs1362217 | 0.88[EUR][1000 genomes] |
| rs1419875 | 0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs2568920 | 0.92[CEU][hapmap];0.89[JPT][hapmap] |
| rs2568921 | 0.92[EUR][1000 genomes] |
| rs2577347 | 0.94[EUR][1000 genomes] |
| rs2577354 | 0.82[EUR][1000 genomes] |
| rs2577356 | 0.93[CEU][hapmap];0.82[EUR][1000 genomes] |
| rs2577358 | 0.83[EUR][1000 genomes] |
| rs2577361 | 0.88[EUR][1000 genomes] |
| rs758577 | 1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:2 , 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 | esv3449389 | chr10:117806874-118102404 | Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | diseases |
| 2 | nsv832000 | chr10:117944492-118116253 | Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:4)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs10749205 | TRUB1 | cis | parietal | SCAN |
| rs10749205 | PNLIPRP3 | cis | parietal | SCAN |
| rs10749205 | C10orf82 | cis | parietal | SCAN |
| rs10749205 | TBC1D5 | trans | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr10:118046200-118046400 | Enhancers | Adipose Derived Mesenchymal Stem Cell Cultured Cells | ES cell derived |
