About Enhancer
| Enhancer ID: | E_01_197 | |
| Enhancer symbol: | -- | |
| Species: | Human | |
| Position : | chr12:98562692-98566384   |
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| Biosample name: | Induced Pluripotent Stem Cells | |
| Experiment class : | Low+High throughput |
| Enhancer type: | Enhancer | |
| Disease: | Schizophrenia | |
| DO: | DOID:5419 | |
| Mesh: | D012559 | |
| Distance from TSS: | >2KB | |
| Pubmed ID: | 25453756 |
| Enhancer experiment: | 3C | |
| Enhancer experiment description: | We identified 4 SNPs (rs2159100, rs12315711, rs11062170, rs4765905) that are in perfect LD with rs758170 and rs1006737, and lie within two predicted enhancers (spanning 1.4Kb and 1.85Kb), ∼185Kb downstream from the gene’s TSS (Figure 5A, Figure 5B). To identify whether the predicted enhancer region might be capable of forming promoter–enhancer loops, we mapped its physical interaction with the CACNA1C TSS in human dorsolateral prefrontal cortex (n = 6) and hiPSC derived-neurons by chromosome conformation capture (3C) assay. Of the 17 restriction site regions tested, only one displayed an increased interaction with the TSS in human postmortem tissue (Primer #4 in Figure 5A–D). This enhancer region includes rs2159100 (MAF = 0.35, GWAS P value = 1.1 × 10−10) and rs12315711 (MAF=0.35, GWAS P value = 1.1 × 10−10) and demonstrates increased interaction frequency with the CACNA1C promoter (F (16, 83) = 5.52, P = 8 × 10−8). The rs2159100/rs12315711 3C interaction was confirmed in hiPSC derived-neurons (Figure 5D). |
About Target gene
| Target gene : | CACNA1C (CACH2,CACN2,CACNL1A1,CCHL1A1,CaV1.2,LQT8,TS,TS.LQT8) | |
| Strong evidence: | 3C | |
| Less strong evidence: | -- | |
| Target gene experiment description: | We identified 4 SNPs (rs2159100, rs12315711, rs11062170, rs4765905) that are in perfect LD with rs758170 and rs1006737, and lie within two predicted enhancers (spanning 1.4Kb and 1.85Kb), ∼185Kb downstream from the gene’s TSS (Figure 5A, Figure 5B). To identify whether the predicted enhancer region might be capable of forming promoter–enhancer loops, we mapped its physical interaction with the CACNA1C TSS in human dorsolateral prefrontal cortex (n = 6) and hiPSC derived-neurons by chromosome conformation capture (3C) assay. Of the 17 restriction site regions tested, only one displayed an increased interaction with the TSS in human postmortem tissue (Primer #4 in Figure 5A–D). This enhancer region includes rs2159100 (MAF = 0.35, GWAS P value = 1.1 × 10−10) and rs12315711 (MAF=0.35, GWAS P value = 1.1 × 10−10) and demonstrates increased interaction frequency with the CACNA1C promoter (F (16, 83) = 5.52, P = 8 × 10−8). The rs2159100/rs12315711 3C interaction was confirmed in hiPSC derived-neurons (Figure 5D). |
About TF
| TF name : | -- | |
| TF experiment: | -- | |
| TF experiment description: | -- |
About Function
| Enhancer function : | -- |
| Enhancer function experiment: | -- |
| Enhancer function experiment description: |
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About SNP
| SNP ID: | -- | |
| SNP position: | -- |
| SNP experiment: | -- |
Enhancer associated network
The number on yellow line represents the distance between enhancer and target gene
