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LOC112340386 H3K4me1 hESC enhancers GRCh37_chr16:2261749-2262562 and GRCh37_chr16:2262563-2263376 [ Homo sapiens (human) ]

Gene ID: 112340386, updated on 17-Sep-2024

Summary

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Gene symbol
LOC112340386
Gene description
H3K4me1 hESC enhancers GRCh37_chr16:2261749-2262562 and GRCh37_chr16:2262563-2263376
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. Two subregions marked by the H3K4me1 histone modification were validated as active enhancers by ChIP-STARR-seq in primed human embryonic stem cells. An overlapping 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 K562 erythroleukemia cells (group: K562 Activating DNase matched - State 2:TssF, active promoter, flanking TSS/CpG islands). The same subregion also displayed weak activation by Sharpr-MPRA in HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 14:Gen5', transcription transition, highly expressed genes towards 5' end). [provided by RefSeq, Nov 2022]
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Genomic context

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See LOC112340386 in Genome Data Viewer
Location:
16p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (2211748..2213375)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (2234206..2235837)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (2261749..2263376)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene TNF receptor associated factor 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:2227829-2228330 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:2232465-2232965 Neighboring gene CASK interacting protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:2239116-2239884 Neighboring gene MPRA-validated peak2469 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:2254430-2255270 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7034 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:2256110-2256949 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:2256950-2257788 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:2260119-2260309 Neighboring gene MTOR associated protein, LST8 homolog Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10258 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7035 Neighboring gene Sharpr-MPRA regulatory region 5944 Neighboring gene BRICHOS domain containing 5 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:2269932-2270556 Neighboring gene phosphoglycolate phosphatase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7037 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10259 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7038 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10260 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:2275282-2275782 Neighboring gene E4F transcription factor 1 Neighboring gene deoxyribonuclease 1 like 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. 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

  • H3K4me1 hESC enhancer GRCh37_chr16:2261749-2262562
  • H3K4me1 hESC enhancer GRCh37_chr16:2262563-2263376
  • Sharpr-MPRA regulatory region 11897

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_056785.2 

    Range
    101..1728
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    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    2211748..2213375
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    2234206..2235837
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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