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LOC112163615 Sharpr-MPRA regulatory region 4597 [ Homo sapiens (human) ]

Gene ID: 112163615, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112163615
Gene description
Sharpr-MPRA regulatory region 4597
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 H3K4me1 histone modification. 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 17:Gen3', transcription 3' end of genes, highly expressed; more exonic) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC112163615 in Genome Data Viewer
Location:
12q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (57093668..57094240)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (57061540..57062112)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (57487729..57488023)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:57423222-57424059 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6520 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6521 Neighboring gene myosin IA Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:57440635-57441834 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6522 Neighboring gene nuclear envelope integral membrane protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6524 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6523 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4569 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4570 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6525 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4571 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:57485501-57485781 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4572 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4573 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:57488515-57489045 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:57489590-57490426 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:57493803-57494325 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:57495608-57496108 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:57496109-57496609 Neighboring gene NGFI-A binding protein 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:57504271-57505218 Neighboring gene uncharacterized LOC124902946 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:57505219-57506164 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4574 Neighboring gene signal transducer and activator of transcription 6 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6527 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:57521273-57521926 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_29738 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:57527325-57528080 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:57540016-57540944 Neighboring gene LDL receptor related protein 1 Neighboring gene LRP1 antisense RNA

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

  • H3K4me1 hESC enhancer GRCh37_chr12:57487451-57487982

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_056593.2 

    Range
    101..673
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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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    57093668..57094240
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    57061540..57062112
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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