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LOC112163595 H3K27ac hESC enhancers GRCh37_chr12:48099027-48099528 and GRCh37_chr12:48099529-48100028 [ Homo sapiens (human) ]

Gene ID: 112163595, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112163595
Gene description
H3K27ac hESC enhancers GRCh37_chr12:48099027-48099528 and GRCh37_chr12:48099529-48100028
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
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. Two adjacent subregions were validated as as enhancers by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in naive human embryonic stem cells, where they are marked by the H3K27ac histone modification. Another subregion was validated as an 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 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 1:Tss). This locus also includes four accessible chromatin subregions, three of which were validated as silencers and one as an enhancer based on their ability to repress or 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, Jun 2023]
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Genomic context

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Location:
12q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (47705244..47706341)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (47666569..47667666)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (48099749..48100043)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene acireductone dioxygenase 1 pseudogene 3 Neighboring gene STBD1 pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:48030175-48030714 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6256 Neighboring gene RNA polymerase II associated protein 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6258 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6259 Neighboring gene RPAP3 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4394 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4395 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:48131928-48133127 Neighboring gene endonuclease, poly(U) specific Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6260 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6261 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:48146243-48146784 Neighboring gene Sharpr-MPRA regulatory region 8178 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6262 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6263 Neighboring gene Rap guanine nucleotide exchange factor 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:48151874-48152542 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:48152543-48153211 Neighboring gene solute carrier family 48 member 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, Free PMC Article
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, Free PMC Article
  3. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, Free PMC Article

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 6257
  • ATAC-STARR-seq lymphoblastoid silent region 4391
  • ATAC-STARR-seq lymphoblastoid silent region 4392
  • ATAC-STARR-seq lymphoblastoid silent region 4393
  • H3K27ac hESC enhancer GRCh37_chr12:48099027-48099528
  • H3K27ac hESC enhancer GRCh37_chr12:48099529-48100028
  • Sharpr-MPRA regulatory region 11797

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_056578.3 

    Range
    101..1198
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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
    47705244..47706341
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    47666569..47667666
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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