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LOC112163550 P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:31901554-31902753 [ Homo sapiens (human) ]

Gene ID: 112163550, updated on 17-Sep-2024

Summary

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Gene symbol
LOC112163550
Gene description
P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:31901554-31902753
Gene type
biological region
Feature type(s)
regulatory: enhancer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. The major subregion was validated as an active enhancer by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in HCT116 colorectal carcinoma cells, where it was defined as a group 1 enhancer that depends on the BRD2, BRD4, P300/CBP, MED14 and CDK7 cofactors, with strong dependence on P300/CBP. Two subregions were also shown to be active enhancers by ChIP-STARR-seq in primed human embryonic stem cells, where both are associated with the OCT4 and NANOG transcription factors and are marked by the H3K27ac and H3K4me1 histone modifications. A subregion was also validated as a functional enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 5:Enh). This locus also includes two accessible chromatin subregions that were validated as enhancers based on their ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC112163550 in Genome Data Viewer
Location:
12p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (31748620..31749976)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (31625457..31626812)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (31901554..31902910)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene antagonist of mitotic exit network 1 homolog Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6173 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:31871502-31872009 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:31872010-31872516 Neighboring gene stathmin 1 pseudogene 1 Neighboring gene uncharacterized LOC105369722 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4329 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6174 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:31882236-31882868 Neighboring gene CRISPRi-validated cis-regulatory element chr12.953 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:31886154-31887353 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4330 Neighboring gene uncharacterized LOC105369724 Neighboring gene Sharpr-MPRA regulatory region 3097 Neighboring gene IFITM3 pseudogene 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:31919651-31919864 Neighboring gene uncharacterized LOC107984470

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 6176
  • ATAC-STARR-seq lymphoblastoid active region 6177
  • OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:31901740-31902325
  • OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:31902326-31902910
  • Sharpr-MPRA regulatory region 4305

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_056574.3 

    Range
    101..1457
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    31748620..31749976
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    31625457..31626812
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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