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LOC122056881 Sharpr-MPRA regulatory region 1049 [ Homo sapiens (human) ]

Gene ID: 122056881, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122056881
Gene description
Sharpr-MPRA regulatory region 1049
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 naive human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K27ac histone modification. 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 22:ReprW, weaker Polycomb repression). [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC122056881 in Genome Data Viewer
Location:
1p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (56435256..56436071)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (56314095..56314909)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (56901449..56901743)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904186 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1076 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:56835566-56836092 Neighboring gene uncharacterized LOC124904185 Neighboring gene long intergenic non-protein coding RNA 1767 Neighboring gene uncharacterized LOC124904189 Neighboring gene Sharpr-MPRA regulatory region 6809 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:56917723-56918398 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:56918399-56919074 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:56919075-56919750 Neighboring gene Sharpr-MPRA regulatory region 2463 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:56942601-56943374 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:56956069-56956568 Neighboring gene NANOG hESC enhancer GRCh37_chr1:56959749-56960407 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:56975627-56976357 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:56977343-56977844 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:56977845-56978344 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1077 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1078 Neighboring gene phospholipid phosphatase 3 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:56996995-56997730 Neighboring gene Sharpr-MPRA regulatory region 2243 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:57001027-57001670 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:57002869-57003370 Neighboring gene ribosomal protein L21 pseudogene 23

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

  • NANOG-H3K27ac hESC enhancer GRCh37_chr1:56900928-56901542

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_076337.2 

    Range
    101..916
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    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    56435256..56436071
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    56314095..56314909
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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