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LOC127406603 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:74405769-74406483 [ Homo sapiens (human) ]

Gene ID: 127406603, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127406603
Gene description
H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:74405769-74406483
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 was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in primed human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. 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 LOC127406603 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (73696046..73696760)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (74874036..74874750)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (74405769..74406483)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17337 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17336 Neighboring gene EEF1A1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24751 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24752 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:74273247-74273796 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:74275447-74275996 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:74285738-74286453 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:74289636-74290835 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:74291165-74292007 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94401 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94402 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94403 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94405 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:74329139-74329367 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:74333473-74333650 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94408 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94412 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94411 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94413 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94414 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94416 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94418 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17338 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24754 Neighboring gene solute carrier family 17 member 5 Neighboring gene Sharpr-MPRA regulatory region 11313 Neighboring gene ribosomal protein S27 pseudogene 15 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24755 Neighboring gene MPRA-validated peak5902 silencer Neighboring gene CD109 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 9272 Neighboring gene MPRA-validated peak5903 silencer Neighboring gene CD109 molecule Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:74550244-74550817 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:74560911-74561502 Neighboring gene uncharacterized LOC101928516 Neighboring gene thioredoxin pseudogene 7 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94479 Neighboring gene family with sequence similarity 136 member A pseudogene

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 17339

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_108574.1 

    Range
    101..815
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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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    73696046..73696760
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    74874036..74874750
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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