Variant report
| Variant | rs1113169 |
|---|---|
| Chromosome Location | chr2:86635502-86635503 |
| allele | A/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 |
rSNPs within LD-proxies of this variant (count:23)
| rs_ID | r2[population] |
|---|---|
| rs10169091 | 1.00[JPT][hapmap] |
| rs10178917 | 0.93[ASN][1000 genomes] |
| rs10180036 | 0.85[CHB][hapmap];0.87[JPT][hapmap] |
| rs11127034 | 0.84[ASN][1000 genomes] |
| rs11678201 | 0.84[AMR][1000 genomes];0.89[EUR][1000 genomes] |
| rs11687162 | 0.89[CEU][hapmap] |
| rs11903855 | 0.88[CEU][hapmap] |
| rs12617075 | 1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[ASN][1000 genomes] |
| rs12714181 | 0.88[JPT][hapmap] |
| rs12714186 | 0.85[CHB][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap] |
| rs13035266 | 1.00[ASN][1000 genomes] |
| rs13383096 | 0.98[ASN][1000 genomes] |
| rs2113607 | 1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes] |
| rs2292887 | 0.85[CHB][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap] |
| rs4832278 | 1.00[CEU][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes] |
| rs4832279 | 0.84[ASN][1000 genomes] |
| rs4832280 | 0.84[ASN][1000 genomes] |
| rs4832282 | 1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[ASN][1000 genomes] |
| rs6713586 | 0.92[CEU][hapmap];0.82[CHB][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.83[EUR][1000 genomes] |
| rs6756146 | 0.92[CEU][hapmap] |
| rs766285 | 0.94[JPT][hapmap] |
| rs908791 | 1.00[ASN][1000 genomes] |
| rs958561 | 0.85[CHB][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap] |
Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | esv3412938 | chr2:86370969-86867936 | Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 77 gene(s) | inside rSNPs | diseases |
| 2 | nsv532724 | chr2:86622295-87086407 | Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 45 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:7)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs1113169 | PTCD3 | cis | cerebellum | SCAN |
| rs1113169 | KDM3A | cis | parietal | SCAN |
| rs1113169 | VPS24 | Cis_1M | lymphoblastoid | RTeQTL |
| rs1113169 | POLR1A | cis | parietal | SCAN |
| rs1113169 | POLR1A | cis | cerebellum | SCAN |
| rs1113169 | KDM3A | cis | cerebellum | SCAN |
| rs1113169 | RNF103 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr2:86635000-86635600 | Enhancers | Primary T helper naive cells from peripheral blood | blood |
| 2 | chr2:86635000-86635800 | Enhancers | Primary T cells from cord blood | blood |
| 3 | chr2:86635000-86635800 | Enhancers | Primary T helper cells PMA-I stimulated | -- |
