Variant report
Variant | rs6495309 |
---|---|
Chromosome Location | chr15:78915245-78915246 |
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:
1
No. | Distal block | Cell Line | Cell type | Cell Stage |
---|---|---|---|---|
1 | chr15:78904939..78907078-chr15:78914502..78917273,2 | K562 | blood: |
No data |
No data |
No data |
No data |
rs_ID | r2[population] |
---|---|
rs11072768 | 0.83[MEX][hapmap] |
rs11637630 | 0.94[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes] |
rs12441998 | 0.83[MEX][hapmap];0.83[TSI][hapmap] |
rs12593950 | 0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes] |
rs12910984 | 0.94[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes] |
rs13329271 | 0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes] |
rs1948 | 0.86[JPT][hapmap] |
rs2456020 | 0.84[EUR][1000 genomes] |
rs28534575 | 0.92[AMR][1000 genomes];0.91[EUR][1000 genomes] |
rs28669908 | 0.82[EUR][1000 genomes] |
rs3743078 | 0.94[CEU][hapmap];0.90[EUR][1000 genomes] |
rs3825845 | 0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes] |
rs4887069 | 0.82[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes] |
rs4887072 | 0.88[AMR][1000 genomes];0.84[EUR][1000 genomes] |
rs518425 | 0.83[CEU][hapmap] |
rs569207 | 0.88[CEU][hapmap];0.82[GIH][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes] |
rs576982 | 0.86[EUR][1000 genomes] |
rs578776 | 0.84[CEU][hapmap];0.84[MEX][hapmap] |
rs637137 | 0.87[CEU][hapmap];0.88[EUR][1000 genomes] |
rs6495308 | 0.94[CEU][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes] |
rs667282 | 0.88[CEU][hapmap];0.80[GIH][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes] |
rs7170068 | 0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes] |
rs7177514 | 0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes] |
rs7183604 | 0.85[AMR][1000 genomes];0.89[EUR][1000 genomes] |
rs7359276 | 0.87[EUR][1000 genomes] |
rs8042059 | 0.94[CEU][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes] |
rs8042374 | 0.94[CEU][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes] |
rs8042494 | 0.86[AMR][1000 genomes];0.91[EUR][1000 genomes] |
rs8043009 | 0.84[AMR][1000 genomes];0.91[EUR][1000 genomes] |
rs938682 | 0.94[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][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 | nsv917303 | chr15:78491050-79205255 | Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 122 gene(s) | inside rSNPs | diseases |
2 | nsv1045827 | chr15:78907656-79004642 | Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 8 gene(s) | inside rSNPs | diseases |
3 | nsv457208 | chr15:78908032-79019610 | Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 10 gene(s) | inside rSNPs | diseases |
4 | nsv570201 | chr15:78908032-79019610 | Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 10 gene(s) | inside rSNPs | diseases |
5 | nsv570202 | chr15:78915245-78953785 | Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 6 gene(s) | inside rSNPs | diseases |
SNP | Gene | Cis/trans | Tissue | Source |
---|---|---|---|---|
rs6495309 | RP11-650L12.2 | cis | Muscle Skeletal | GTEx |
rs6495309 | PSMA4 | cis | parietal | SCAN |
rs6495309 | CHRNA5 | cis | cerebellum | SCAN |
rs6495309 | PSMA4 | cis | cerebellum | SCAN |
rs6495309 | COX5A | cis | parietal | SCAN |
rs6495309 | NPTN | cis | cerebellum | SCAN |
rs6495309 | CHRNA5 | cis | Muscle Skeletal | GTEx |
No. | Chromosome Location | Chromatin state | Cell line | Tissue |
---|---|---|---|---|
1 | chr15:78914800-78921600 | Enhancers | Fetal Thymus | thymus |
2 | chr15:78915000-78917400 | Enhancers | Thymus | Thymus |
3 | chr15:78915000-78929600 | Weak transcription | ES-UCSF4 Cell Line | embryonic stem cell |