Variant report
Variant | rs6042480 |
---|---|
Chromosome Location | chr20:13998080-13998081 |
allele | C/T |
Outlinks | Ensembl   UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
No data |
No data |
No data |
No data |
No data |
No data |
No data |
rs_ID | r2[population] |
---|---|
rs13039593 | 1.00[LWK][hapmap] |
rs2423761 | 1.00[LWK][hapmap] |
rs243910 | 1.00[LWK][hapmap] |
rs6033866 | 0.93[AFR][1000 genomes];1.00[AMR][1000 genomes] |
rs6033892 | 1.00[YRI][hapmap] |
rs6033894 | 1.00[LWK][hapmap];1.00[YRI][hapmap] |
rs6033895 | 1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes] |
rs6033899 | 0.81[AFR][1000 genomes];1.00[AMR][1000 genomes] |
rs6042426 | 1.00[LWK][hapmap] |
rs6042472 | 1.00[AMR][1000 genomes] |
rs6042477 | 0.94[AFR][1000 genomes];1.00[AMR][1000 genomes] |
rs6042502 | 1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes] |
rs6042526 | 0.83[AFR][1000 genomes];1.00[AMR][1000 genomes] |
rs6042542 | 1.00[LWK][hapmap];1.00[YRI][hapmap] |
rs6042545 | 1.00[YRI][hapmap] |
rs6042551 | 1.00[AMR][1000 genomes] |
rs6042557 | 0.83[LWK][hapmap];1.00[AMR][1000 genomes] |
rs6042562 | 1.00[YRI][hapmap] |
rs6042579 | 0.81[AFR][1000 genomes];1.00[AMR][1000 genomes] |
rs6042586 | 1.00[LWK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes] |
rs73255017 | 1.00[AMR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page:
1
No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
---|---|---|---|---|---|---|---|
1 | nsv916202 | chr20:13421724-14043615 | Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 13 gene(s) | inside rSNPs | diseases |
2 | nsv1066810 | chr20:13451869-14432454 | Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 17 gene(s) | inside rSNPs | diseases |
3 | nsv912689 | chr20:13570331-14155881 | Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 14 gene(s) | inside rSNPs | diseases |
4 | nsv531479 | chr20:13632491-14434432 | Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 16 gene(s) | inside rSNPs | diseases |
5 | nsv526954 | chr20:13995214-14055947 | Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS | Chromatin interactive region | 2 gene(s) | inside rSNPs | diseases |
SNP | Gene | Cis/trans | Tissue | Source |
---|---|---|---|---|
rs6042480 | ULK2 | trans | lymphoblastoid | seeQTL |
rs6042480 | CSTA | trans | lymphoblastoid | seeQTL |
rs6042480 | FOXG1 | trans | lymphoblastoid | seeQTL |
rs6042480 | SCT | trans | lymphoblastoid | seeQTL |
rs6042480 | CYB5R2 | trans | lymphoblastoid | seeQTL |
rs6042480 | SNRNP35 | trans | lymphoblastoid | seeQTL |
No. | Chromosome Location | Chromatin state | Cell line | Tissue |
---|---|---|---|---|
1 | chr20:13998000-14000600 | Weak transcription | hESC Derived CD56+ Ectoderm Cultured Cells | ES cell derived |