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LOC121627819 Sharpr-MPRA regulatory region 3542 [ Homo sapiens (human) ]

Gene ID: 121627819, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121627819
Gene description
Sharpr-MPRA regulatory region 3542
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. It was validated as a functional enhancer by the Sharpr-MPRA technique (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 12:CtcfO, distal CTCF/candidate insulator with open chromatin) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Jun 2021]
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Genomic context

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See LOC121627819 in Genome Data Viewer
Location:
17q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (80575349..80575643)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (81476779..81477073)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (78549149..78549443)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78441725-78442449 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78448861-78449394 Neighboring gene Sharpr-MPRA regulatory region 3125 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78467323-78467823 Neighboring gene neuronal pentraxin 1 Neighboring gene Sharpr-MPRA regulatory region 6979 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78500540-78501513 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:78509630-78510257 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78518332-78519158 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78519159-78519985 Neighboring gene MPRA-validated peak3025 silencer Neighboring gene uncharacterized LOC105371922 Neighboring gene ribosomal protein L32 pseudogene 31 Neighboring gene regulatory associated protein of MTOR complex 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78587247-78587748 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78587749-78588248 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78589766-78590266 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78590267-78590767 Neighboring gene MPRA-validated peak3026 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78610889-78611669 Neighboring gene ribosomal protein L31 pseudogene 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78634706-78635206 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78635207-78635707 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78650012-78650538 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78650539-78651063 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr17:78667505-78668704 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78670527-78671054 Neighboring gene Sharpr-MPRA regulatory region 1160 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12939 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:78694608-78695807 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78699572-78700532 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12940 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12941 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:78717414-78717768 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78722091-78722592 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78722593-78723092 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:78734834-78736033 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12943 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78753273-78753773 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12944 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9110 Neighboring gene uncharacterized LOC101928855

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

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)

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_075009.1 

    Range
    101..395
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    80575349..80575643
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    81476779..81477073
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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