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LOC112577495 Sharpr-MPRA regulatory region 4766 [ Homo sapiens (human) ]

Gene ID: 112577495, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112577495
Gene description
Sharpr-MPRA regulatory region 4766
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 (MPRA) 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 non-DNase unmatched - State 22:ReprW, weaker Polycomb repression) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate 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:
1q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (154859790..154860527)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (153999128..153999865)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (154832709..154833003)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904428 Neighboring gene potassium calcium-activated channel subfamily N member 3 Neighboring gene uncharacterized LOC124904429 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:154702946-154703755 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:154703756-154704564 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:154708005-154708564 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:154708837-154710036 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:154714090-154714590 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1782 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:154721874-154722377 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1365 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1366 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1783 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:154785391-154786050 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:154786051-154786708 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:154812853-154813354 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1784 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1785 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1786 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:154831699-154832199 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:154834547-154835222 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:154835223-154835896 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1788 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:154836963-154837852 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1789 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:154840581-154841100 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:154842508-154843464 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:154849802-154850387 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:154850973-154851557 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:154883471-154883971 Neighboring gene uncharacterized LOC105371449 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:154908701-154909643 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:154909644-154910585 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1368 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:154914379-154915254 Neighboring gene phosphomevalonate kinase

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. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, Free PMC Article
  3. 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

  • ATAC-STARR-seq lymphoblastoid active region 1787
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:154832266-154832879

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_060200.2 

    Range
    101..838
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    154859790..154860527
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    153999128..153999865
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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