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LOC127897180 H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:9982293-9983176 [ Homo sapiens (human) ]

Gene ID: 127897180, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127897180
Gene description
H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:9982293-9983176
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 naive 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 LOC127897180 in Genome Data Viewer
Location:
chromosome: X
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (10014253..10015136)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (9596785..9597668)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (9982293..9983176)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene shroom family member 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:9833462-9834428 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:9834429-9835394 Neighboring gene high mobility group nucleosome binding domain 1 pseudogene 33 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:9891143-9891644 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:9891645-9892144 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:9895839-9896557 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chrX:9907403-9908602 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:9908687-9909186 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29404 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29405 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29406 Neighboring gene claudin 34 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:9981409-9982292 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20655 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:10008750-10009284 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:10009285-10009817 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:10014897-10015530 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:10015531-10016163 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:10018119-10018742 Neighboring gene WWC family member 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:10050926-10051426 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29407 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:10077459-10078176 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:10078177-10078894 Neighboring gene Sharpr-MPRA regulatory region 7563 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:10141885-10142861 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20656 Neighboring gene chloride voltage-gated channel 4

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 20654

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_146665.1 

    Range
    101..984
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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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    10014253..10015136
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    9596785..9597668
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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