Variant report
| Variant | rs10880220 |
|---|---|
| Chromosome Location | chr12:42383046-42383047 |
| 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 | chr12:42381754..42384165-chr12:42384575..42386988,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:15)
| rs_ID | r2[population] |
|---|---|
| rs1059360 | 0.82[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.87[MKK][hapmap] |
| rs10880230 | 0.81[AMR][1000 genomes] |
| rs10880259 | 0.85[JPT][hapmap] |
| rs10880260 | 0.85[CHB][hapmap];0.85[JPT][hapmap] |
| rs10880261 | 0.85[JPT][hapmap] |
| rs11181289 | 0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes] |
| rs11181308 | 0.81[AMR][1000 genomes];0.80[EUR][1000 genomes] |
| rs11181328 | 0.91[CEU][hapmap];0.95[CHB][hapmap] |
| rs11181364 | 0.84[JPT][hapmap] |
| rs12371615 | 0.82[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.87[MKK][hapmap] |
| rs12372597 | 0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs3229 | 0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes] |
| rs7312933 | 0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap] |
| rs7957213 | 0.80[AMR][1000 genomes] |
| rs7969415 | 0.81[AMR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv430505 | chr12:42297931-42720773 | Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 38 gene(s) | inside rSNPs | diseases |
| 2 | nsv832387 | chr12:42345541-42465505 | Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:3)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs10880220 | PRICKLE1 | Cis_1M | lymphoblastoid | RTeQTL |
| rs10880220 | BIN1 | trans | lymphoblastoid | seeQTL |
| rs10880220 | GXYLT1 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr12:42383000-42383200 | Bivalent Enhancer | Foreskin Melanocyte Primary Cells skin03 | Skin |
