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LOC121847970 Sharpr-MPRA regulatory region 3169 [ Homo sapiens (human) ]

Gene ID: 121847970, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121847970
Gene description
Sharpr-MPRA regulatory region 3169
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 primed 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 HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
16p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (12142732..12143269)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (12178988..12179525)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (12236589..12236883)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene sorting nexin 29 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10465 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7217 Neighboring gene Sharpr-MPRA regulatory region 9869 Neighboring gene uncharacterized LOC642696 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:12215085-12215584 Neighboring gene ribosomal protein S23 pseudogene 6 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:12241842-12242399 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:12257095-12257595 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:12355210-12355716 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10466 Neighboring gene small nucleolar RNA ACA64 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:12404869-12405376 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:12405377-12405883 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:12407183-12407683 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:12408231-12408918 Neighboring gene Sharpr-MPRA regulatory region 2664 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:12410661-12411592 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:12426104-12426604 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:12435179-12436378 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10467 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7218 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10468 Neighboring gene uncharacterized LOC101927227 Neighboring gene uncharacterized LOC105371087

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_chr16:12236626-12237126

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_075996.2 

    Range
    101..638
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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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    12142732..12143269
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    12178988..12179525
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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