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LOC121627931 Sharpr-MPRA regulatory region 10319 [ Homo sapiens (human) ]

Gene ID: 121627931, updated on 12-Sep-2024

Summary

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Gene symbol
LOC121627931
Gene description
Sharpr-MPRA regulatory region 10319
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. The major subregion was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in naive human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. Another subregion was validated as an enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 25:Art, potential CNV or repetitive artifacts). [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC121627931 in Genome Data Viewer
Location:
22q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (20867421..20868107)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (21276141..21276827)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (21221709..21222395)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13497 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18683 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:21057515-21058087 Neighboring gene transmembrane protein 191A (pseudogene) Neighboring gene phosphatidylinositol 4-kinase alpha Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:21089235-21089736 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13499 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18684 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18685 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18686 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18687 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:21105755-21106552 Neighboring gene Sharpr-MPRA regulatory region 10582 Neighboring gene serpin family D member 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13500 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:21213217-21214026 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:21227050-21227239 Neighboring gene MPRA-validated peak4460 silencer Neighboring gene synaptosome associated protein 29 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:21240059-21240559 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18688 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13502 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18689 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr22:21278919-21279566 Neighboring gene uncharacterized LOC124905167 Neighboring gene CRK like proto-oncogene, adaptor protein Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:21305807-21306308 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:21306309-21306808 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:21310951-21311146 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:21311117-21311712 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18690 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18691 Neighboring gene long intergenic non-protein coding RNA 1637

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

  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:21221864-21222395

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_075122.2 

    Range
    101..787
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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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    20867421..20868107
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    21276141..21276827
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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