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LOC112872296 Sharpr-MPRA regulatory region 2719 [ Homo sapiens (human) ]

Gene ID: 112872296, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112872296
Gene description
Sharpr-MPRA regulatory region 2719
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), with weaker activation in K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Jul 2018]
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Genomic context

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Location:
3q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (126184606..126184900)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (128916970..128917264)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (125903449..125903743)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:125822083-125822904 Neighboring gene ALDH1L1 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:125831607-125832121 Neighboring gene aldehyde dehydrogenase 1 family member L1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:125847779-125848549 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:125850681-125851498 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14674 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:125855703-125856203 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_64577 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:125876969-125877469 Neighboring gene uncharacterized LOC105374083 Neighboring gene RNA, U1 small nuclear 30, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:125899089-125899844 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:125899845-125900598 Neighboring gene ALDH1L1 antisense RNA 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20437 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:125926972-125928171 Neighboring gene uncharacterized LOC124909426 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:125932350-125932862 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:125977069-125977976 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:125985551-125986260 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:125986261-125986971 Neighboring gene uncharacterized LOC107986124 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:126006839-126007384 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126007385-126007929 Neighboring gene KLF transcription factor 15

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_061355.1 

    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    126184606..126184900
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    128916970..128917264
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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