About Enhancer
| Enhancer ID: | E_01_014 | |
| Enhancer symbol: | -- | |
| Species: | Human | |
| Position : | chr6:170855462-170856787   |
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| Biosample name: | HEK-293,β-Cell | |
| Experiment class : | Low+High throughput |
| Enhancer type: | Enhancer | |
| Disease: | Type 2 Diabetes Mellitus | |
| DO: | DOID:9352 | |
| Mesh: | D003924 | |
| Distance from TSS: | >2KB | |
| Pubmed ID: | 24413736 |
| Enhancer experiment: | RNA-seq,ChIP-seq,ChIP,EMSA,PCR,4C,Luciferase Reporter Assay | |
| Enhancer experiment description: | To define enhancer clusters, we first created 1,000 iterations of randomized C3 sites in the mappable genome of individual chromosomes. We then calculated for each chromosome the 25th percentile of inter-site distances of randomized C3 sites (Supplementary Fig. 6a). Next,we defined clusters of islet C3 sites as any group of ≥3 C3 sites in which all adjacent C3 sites were separated by less than the abovementioned 25th percentile distance for randomized sites in the same chromosome. The distribution of islet C3 clusters differed from that of clusters generated with randomized C3 sites (Supplementary Fig. 6b) |
About Target gene
| Target gene : | TBP(GTF2D,GTF2D1,HDL4,SCA17,TFIID) | |
| Strong evidence: | 4C | |
| Less strong evidence: | RNA-seq,ChIP-seq,ChIP,EMSA,PCR,Luciferase Reporter Assay | |
| Target gene experiment description: | islet-specific gene loci showed an increased density of islet transcription factor-bound active enhancer (C3) accessible chromatin sites. |
About TF
| TF name : | FOXA2(HNF3B,TCF3B)MAFB(DURS3,KRML,MCTO)NKX2-2(NKX2.2,NKX2B) | |
| TF experiment: | ChIP-seq | |
| TF experiment description: | To determine the genomic binding sites of these islet transcription factors, we used chromatin immunoprecipitation and sequencing(ChIP-seq) in duplicate human islet samples and identified 3,911-32,747 high-confidence sites per transcription factor. |
About Function
| Enhancer function : | Sequence variants associated with type 2 diabetes and fasting glycemia are enriched in these clustered islet enhancers and identify trait-associated variants that disrupt DNA binding and islet enhancer activity. |
| Enhancer function experiment: | Luciferase Reporter Assay |
| Enhancer function experiment description: |
Transcription factor-bound C3 sites were also cloned in Gateway-adapted PGL4.23 and cotransfected in triplicate wells with pRL in MIN6 and 3T3 cells, and luciferase activity was measured after 48 hr. Results were expressed as luciferase/renilla ratios in vectors carrying putative Enhancers, relative to the ratio in empty PGL4.23 vector. |
About SNP
| SNP ID: | rs58692659 | |
| SNP position: | 37775652 |
| SNP experiment: | Luciferase Reporter Assay,EMSA |
Enhancer associated network
The number on yellow line represents the distance between enhancer and target gene
