Variant report
| Variant | rs12578369 |
|---|---|
| Chromosome Location | chr12:22227229-22227230 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:2)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:2 , 50 per page) page:
1
| No data |
(count:1 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr12:22223038..22225201-chr12:22226314..22228926,2 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ST8SIA1 | TF binding region |
| ENSG00000111728 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:19)
| rs_ID | r2[population] |
|---|---|
| rs12423101 | 1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes] |
| rs12423142 | 0.83[AMR][1000 genomes];0.98[ASN][1000 genomes] |
| rs12424838 | 0.89[AMR][1000 genomes];0.98[ASN][1000 genomes] |
| rs12427354 | 1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes] |
| rs12816385 | 0.83[AMR][1000 genomes];0.91[ASN][1000 genomes] |
| rs12818845 | 0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs2193379 | 0.88[AMR][1000 genomes];0.97[ASN][1000 genomes] |
| rs2418036 | 0.97[ASN][1000 genomes] |
| rs6487271 | 0.98[ASN][1000 genomes] |
| rs6487278 | 0.99[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs67339960 | 0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs71448623 | 0.84[AMR][1000 genomes];0.95[ASN][1000 genomes] |
| rs7299120 | 0.82[EUR][1000 genomes] |
| rs7300481 | 0.98[ASN][1000 genomes] |
| rs7606 | 1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes] |
| rs7954234 | 1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes] |
| rs7956642 | 1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes] |
| rs7969132 | 0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs7978726 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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 | nsv1051073 | chr12:21910875-22271209 | Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 18 gene(s) | inside rSNPs | diseases |
| 2 | esv2758298 | chr12:22140834-22339299 | Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 11 gene(s) | inside rSNPs | diseases |
| 3 | esv2759883 | chr12:22140834-22736907 | Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 29 gene(s) | inside rSNPs | diseases |
| 4 | nsv438196 | chr12:22195202-22234058 | Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 9 gene(s) | inside rSNPs | diseases |
| 5 | esv1850259 | chr12:22198865-22244741 | Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 9 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:3)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs12578369 | LST-3TM12 | cis | cerebellum | SCAN |
| rs12578369 | CMAS | cis | cerebellum | SCAN |
| rs12578369 | RASSF8 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr12:22203800-22235200 | Weak transcription | Gastric | stomach |
| 2 | chr12:22209800-22229200 | Weak transcription | Thymus | Thymus |
| 3 | chr12:22216200-22233200 | Weak transcription | K562 | blood |
