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LOC121627941 H3K27ac-H3K4me1 hESC enhancers GRCh37_chr22:39409474-39410092 and GRCh37_chr22:39410093-39410710 [ Homo sapiens (human) ]

Gene ID: 121627941, updated on 12-Sep-2024

Summary

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Gene symbol
LOC121627941
Gene description
H3K27ac-H3K4me1 hESC enhancers GRCh37_chr22:39409474-39410092 and GRCh37_chr22:39410093-39410710
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. Two subregions marked by the H3K27ac and H3K4me1 histone modifications were validated as active enhancers by ChIP-STARR-seq in primed human embryonic stem cells. An overlapping 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 K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). This locus also includes two accessible chromatin subregions, one of which was validated as an enhancer and the other as a silencer based on their ability to activate or 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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Location:
22q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (39013469..39014705)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (39483881..39485117)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (39409474..39410710)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124905118 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39370179-39370956 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13737 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr22:39380734-39381933 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:39382500-39382695 Neighboring gene apolipoprotein B mRNA editing enzyme catalytic subunit 3B Neighboring gene APOBEC3B antisense RNA 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr22:39394090-39394730 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39406643-39407144 Neighboring gene apolipoprotein B mRNA editing enzyme catalytic subunit 3C Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39415894-39416734 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39417574-39418413 Neighboring gene apolipoprotein B mRNA editing enzyme catalytic subunit 3D Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39423978-39424906 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39426361-39427157 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr22:39432783-39433673 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19027 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39437791-39438568 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:39439415-39439645 Neighboring gene apolipoprotein B mRNA editing enzyme catalytic subunit 3F Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr22:39445317-39446516 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13739 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39448525-39449459

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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 active region 19025
  • ATAC-STARR-seq lymphoblastoid silent region 13738
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39409474-39410092
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39410093-39410710
  • Sharpr-MPRA regulatory region 8537

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_075132.2 

    Range
    101..1337
    Download
    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    39013469..39014705
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    39483881..39485117
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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