Variant report
| Variant | rs2638269 |
|---|---|
| Chromosome Location | chr12:40541197-40541198 |
| allele | A/C |
| Outlinks | Ensembl UCSC |
- TF binding region (count:1)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:1 , 50 per page) page:
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| Variant related genes | Relation type |
|---|---|
| ENSG00000260943 | TF binding region |
rSNPs within LD-proxies of this variant (count:27)
| rs_ID | r2[population] |
|---|---|
| rs10878208 | 0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs11175332 | 0.89[ASN][1000 genomes] |
| rs11175371 | 0.89[ASN][1000 genomes] |
| rs11175401 | 0.82[ASN][1000 genomes] |
| rs11175405 | 0.95[ASN][1000 genomes] |
| rs11175422 | 0.81[ASN][1000 genomes] |
| rs11175458 | 0.85[ASN][1000 genomes] |
| rs12581617 | 0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs1491922 | 0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs1491923 | 0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs1491925 | 0.95[ASN][1000 genomes] |
| rs17443199 | 0.84[ASN][1000 genomes] |
| rs17461429 | 0.82[ASN][1000 genomes] |
| rs2046931 | 0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs2253736 | 0.91[ASN][1000 genomes] |
| rs2638222 | 0.81[AFR][1000 genomes] |
| rs2638224 | 0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs2638244 | 0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes] |
| rs2638247 | 0.95[ASN][1000 genomes] |
| rs2638250 | 0.91[ASN][1000 genomes] |
| rs2638268 | 0.99[ASN][1000 genomes] |
| rs2638270 | 0.89[ASN][1000 genomes] |
| rs2638271 | 0.99[ASN][1000 genomes] |
| rs2708463 | 0.99[ASN][1000 genomes] |
| rs2708465 | 0.96[ASN][1000 genomes] |
| rs2708478 | 0.91[ASN][1000 genomes] |
| rs7310104 | 0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:5 , 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 | nsv558596 | chr12:40413698-40591117 | Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 14 gene(s) | inside rSNPs | diseases |
| 2 | nsv899030 | chr12:40509341-40580440 | Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 8 gene(s) | inside rSNPs | diseases |
| 3 | nsv899031 | chr12:40520684-40580440 | Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 8 gene(s) | inside rSNPs | diseases |
| 4 | esv3379462 | chr12:40539260-40541633 | Enhancers Weak transcription | TF binding region | 1 gene(s) | inside rSNPs | n/a |
| 5 | esv3325031 | chr12:40539585-40541333 | Enhancers Weak transcription | TF binding region | 1 gene(s) | inside rSNPs | n/a |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs2638269 | LRRK2 | cis | Muscle Skeletal | GTEx |
| rs2638269 | RP11-476D10.1 | cis | Whole Blood | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr12:40532800-40543800 | Weak transcription | Breast variant Human Mammary Epithelial Cells (vHMEC) | Breast |
| 2 | chr12:40540800-40541400 | Enhancers | Primary monocytes fromperipheralblood | blood |
| 3 | chr12:40541000-40541800 | Enhancers | Monocytes-CD14+_RO01746 | blood |
