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LOC124310647 Sharpr-MPRA regulatory region 8141 [ Homo sapiens (human) ]

Gene ID: 124310647, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124310647
Gene description
Sharpr-MPRA regulatory region 8141
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. The major subregion was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in primed human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. Another subregion was validated as a repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 20:ReprD, Polycomb repression w. Duke DNase/promoter and conservation enriched). [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
9q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (126665430..126666441)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (138870856..138871867)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (129427709..129428003)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129350903-129351737 Neighboring gene uncharacterized LOC124902272 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:129370112-129370312 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:129372327-129373191 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20289 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129375135-129376103 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129376359-129376940 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129376941-129377520 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129378101-129378680 Neighboring gene LMX1B divergent transcript Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:129387803-129388768 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129392623-129393190 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129393191-129393758 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129398978-129399478 Neighboring gene LIM homeobox transcription factor 1 beta Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129414454-129415333 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129416491-129416990 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129424890-129425503 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129425974-129426490 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129426491-129427005 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129436714-129437369 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr9:129438749-129439277 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr9:129439278-129439806 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129445577-129446297 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:129450160-129451042 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:129456574-129457344 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:129458734-129459234 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129464425-129465019 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr9:129467063-129467788 and GRCh37_chr9:129467789-129468514 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129468515-129469238 Neighboring gene uncharacterized LOC107987129 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129482087-129482586 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29018 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20290 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20291 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_106693 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_106710 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20292 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:129567045-129567546 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29019 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29020 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29021 Neighboring gene zinc finger and BTB domain containing 43 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129594985-129595486 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129595487-129595986

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_chr9:129427881-129428720

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_078928.2 

    Range
    101..1112
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    126665430..126666441
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    138870856..138871867
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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