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LOC112136100 H3K4me1 hESC enhancer GRCh37_chr12:1913659-1914581 [ Homo sapiens (human) ]

Gene ID: 112136100, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112136100
Gene description
H3K4me1 hESC enhancer GRCh37_chr12:1913659-1914581
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. It was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in naive human embryonic stem cells, where it is marked by the H3K4me1 histone modification. A subregion was also 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 18:Pol2, Pol2 specific locations, majority in genes but substantial portion in intergenic locations) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin). This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to repress 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 LOC112136100 in Genome Data Viewer
Location:
12p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (1804493..1805415)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (1800633..1801555)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (1913709..1914003)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene SDA1 domain containing 1 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4122 Neighboring gene adiponectin receptor 2 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:1854087-1854680 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:1875063-1875563 Neighboring gene ribosomal protein S4X pseudogene 14 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:1885224-1885742 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:1885743-1886260 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:1904713-1905280 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:1905392-1906297 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:1906298-1907202 Neighboring gene uncharacterized LOC105369602 Neighboring gene calcium voltage-gated channel auxiliary subunit alpha2delta 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5812 Neighboring gene uncharacterized LOC105369601 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:1929301-1930047 Neighboring gene Sharpr-MPRA regulatory region 2999 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:1937325-1937864 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:1939727-1940340 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:1944610-1945110 Neighboring gene leucine rich repeats and transmembrane domains 2

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 silent region 4126
  • Sharpr-MPRA regulatory region 5038

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_056537.2 

    Range
    101..1023
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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
    1804493..1805415
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_018654718.1 Reference GRCh38.p14 PATCHES

    Range
    146637..147559
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    1800633..1801555
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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