Variant report
| Variant | rs6879074 |
|---|---|
| Chromosome Location | chr5:17338372-17338373 |
| allele | G/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 | chr5:17336392..17339049-chr5:17358419..17360973,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:1)
| rs_ID | r2[population] |
|---|---|
| rs56663279 | 0.89[AFR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1029959 | chr5:17133214-17455995 | Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 38 gene(s) | inside rSNPs | diseases |
| 2 | nsv461988 | chr5:17296342-17484038 | Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 26 gene(s) | inside rSNPs | diseases |
| 3 | nsv597313 | chr5:17296342-17484038 | Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 26 gene(s) | inside rSNPs | diseases |
| 4 | nsv830219 | chr5:17325802-17518914 | Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 32 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:64)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs6879074 | MERTK | cis | Liver | GTEx |
| rs6879074 | NM_173463 | trans | multi-tissue | Pritchard |
| rs6879074 | LRP1B | cis | Liver | GTEx |
| rs6879074 | PLXNA2 | cis | Liver | GTEx |
| rs6879074 | C20orf71 | trans | multi-tissue | Pritchard |
| rs6879074 | AF091236 | trans | multi-tissue | Pritchard |
| rs6879074 | BC035235 | trans | multi-tissue | Pritchard |
| rs6879074 | SESN1 | cis | Liver | GTEx |
| rs6879074 | ITGB4 | cis | Liver | GTEx |
| rs6879074 | HSS00165977 | trans | multi-tissue | Pritchard |
| rs6879074 | FBXL6 | trans | multi-tissue | Pritchard |
| rs6879074 | BAI2 | trans | multi-tissue | Pritchard |
| rs6879074 | THOC5 | cis | Liver | GTEx |
| rs6879074 | XM_106715 | trans | multi-tissue | Pritchard |
| rs6879074 | HSS00043702 | trans | multi-tissue | Pritchard |
| rs6879074 | AK097788 | trans | multi-tissue | Pritchard |
| rs6879074 | MUC6 | trans | multi-tissue | Pritchard |
| rs6879074 | BAI2 | cis | Liver | GTEx |
| rs6879074 | LOC100131354 | cis | Liver | GTEx |
| rs6879074 | NEK7 | cis | Liver | GTEx |
| rs6879074 | MUC6 | cis | Liver | GTEx |
| rs6879074 | C1orf189 | cis | Liver | GTEx |
| rs6879074 | Contig29142_RC | trans | multi-tissue | Pritchard |
| rs6879074 | SPN | trans | multi-tissue | Pritchard |
| rs6879074 | SCN2B | cis | Liver | GTEx |
| rs6879074 | Contig56010_RC | trans | multi-tissue | Pritchard |
| rs6879074 | ZNF662 | trans | multi-tissue | Pritchard |
| rs6879074 | PLA2G1B | cis | Liver | GTEx |
| rs6879074 | SPN | cis | Liver | GTEx |
| rs6879074 | C1orf189 | trans | multi-tissue | Pritchard |
| rs6879074 | MERTK | trans | multi-tissue | Pritchard |
| rs6879074 | ZNF662 | cis | Liver | GTEx |
| rs6879074 | C20orf71 | cis | Liver | GTEx |
| rs6879074 | Contig40858_RC | trans | multi-tissue | Pritchard |
| rs6879074 | MMP25 | cis | Liver | GTEx |
| rs6879074 | AF086525 | trans | multi-tissue | Pritchard |
| rs6879074 | GAL3ST3 | trans | multi-tissue | Pritchard |
| rs6879074 | XM_212332 | trans | multi-tissue | Pritchard |
| rs6879074 | HSS00123860 | trans | multi-tissue | Pritchard |
| rs6879074 | SLC39A4 | cis | Liver | GTEx |
| rs6879074 | hCT2274079 | trans | multi-tissue | Pritchard |
| rs6879074 | OR1J4 | cis | Liver | GTEx |
| rs6879074 | ZNF208 | trans | multi-tissue | Pritchard |
| rs6879074 | CCDC149 | cis | Liver | GTEx |
| rs6879074 | hCG_2015435 | cis | Liver | GTEx |
| rs6879074 | LOC138412 | cis | Liver | GTEx |
| rs6879074 | BNC2 | cis | Liver | GTEx |
| rs6879074 | C6orf25 | cis | Liver | GTEx |
| rs6879074 | PLA2G1B | trans | multi-tissue | Pritchard |
| rs6879074 | DLGAP1 | cis | Liver | GTEx |
| rs6879074 | ITGB4 | trans | multi-tissue | Pritchard |
| rs6879074 | SLC39A4 | trans | multi-tissue | Pritchard |
| rs6879074 | OR1J4 | trans | multi-tissue | Pritchard |
| rs6879074 | FBXL6 | cis | Liver | GTEx |
| rs6879074 | ZNF208 | cis | Liver | GTEx |
| rs6879074 | hCT2267103 | cis | multi-tissue | Pritchard |
| rs6879074 | C6orf25 | trans | multi-tissue | Pritchard |
| rs6879074 | XM_173794 | trans | multi-tissue | Pritchard |
| rs6879074 | THOC5 | trans | multi-tissue | Pritchard |
| rs6879074 | XM_212462 | trans | multi-tissue | Pritchard |
| rs6879074 | SCN2B | trans | multi-tissue | Pritchard |
| rs6879074 | XM_069557 | trans | multi-tissue | Pritchard |
| rs6879074 | BNC2 | trans | multi-tissue | Pritchard |
| rs6879074 | GAL3ST3 | cis | Liver | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr5:17336600-17339400 | ZNF genes & repeats | hESC Derived CD184+ Endoderm Cultured Cells | ES cell derived |
