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LOC127824375 H3K4me1 hESC enhancer GRCh37_chr12:57609975-57610474 [ Homo sapiens (human) ]

Gene ID: 127824375, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127824375
Gene description
H3K4me1 hESC enhancer GRCh37_chr12:57609975-57610474
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 region includes an enhancer that was validated 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. 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 LOC127824375 in Genome Data Viewer
Location:
chromosome: 12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (57216192..57216816)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (57184440..57185064)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (57609975..57610599)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene LDL receptor related protein 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:57540016-57540944 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:57542802-57543729 Neighboring gene LRP1 antisense RNA Neighboring gene Sharpr-MPRA regulatory region 9665 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:57566901-57567114 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:57570347-57571546 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4575 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:57586343-57586842 Neighboring gene microRNA 1228 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4576 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:57608455-57608977 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:57610622-57611230 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:57611231-57611837 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:57617093-57617999 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4578 Neighboring gene neurexophilin 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6528 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6529 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6530 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:57624967-57625547 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:57625548-57626129 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:57626711-57627291 Neighboring gene Sharpr-MPRA regulatory region 225 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6532 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:57631624-57632226 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4579 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:57633295-57634200 Neighboring gene NDUFA4 mitochondrial complex associated like 2 Neighboring gene serine hydroxymethyltransferase 2 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr12:57636011-57636914 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6534 Neighboring gene SH3 and cysteine rich domain 3

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. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. PMID 35858748, 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 Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 4577

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_125892.2 

    Range
    101..725
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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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    57216192..57216816
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    57184440..57185064
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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