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LOC112939930 Sharpr-MPRA regulatory region 10599 [ Homo sapiens (human) ]

Gene ID: 112939930, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112939930
Gene description
Sharpr-MPRA regulatory region 10599
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 HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Aug 2018]
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Genomic context

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See LOC112939930 in Genome Data Viewer
Location:
4p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (3206082..3206376)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (3204838..3205132)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (3207809..3208103)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21213 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21214 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15198 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15199 Neighboring gene huntingtin repeat instability region Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15200 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21215 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21216 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21217 Neighboring gene HTT antisense RNA Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21218 Neighboring gene RNA, U7 small nuclear 33 pseudogene Neighboring gene huntingtin Neighboring gene ReSE screen-validated silencer GRCh37_chr4:3137138-3137317 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15201 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:3215679-3216179 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:3215178-3215678 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:3239294-3239953 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr4:3239954-3240612 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:3248264-3248439 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:3252404-3253300 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:3271939-3272476 Neighboring gene Myb/SANT DNA binding domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15202 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15203 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15204 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:3295537-3296122 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:3296907-3297102 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21219 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21220 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:3306185-3306834 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:3310051-3310769 Neighboring gene X antigen family member 3 pseudogene Neighboring gene regulator of G protein signaling 12

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_061508.1 

    Range
    101..395
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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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    3206082..3206376
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    3204838..3205132
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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