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LOC112543477 Sharpr-MPRA regulatory region 3019 [ Homo sapiens (human) ]

Gene ID: 112543477, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112543477
Gene description
Sharpr-MPRA regulatory region 3019
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 8:EnhW, candidate weak enhancer and open chromatin) and K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 20:ReprD, Polycomb repression with Duke DNase/promoter and conservation enriched). [provided by RefSeq, May 2018]
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Genomic context

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See LOC112543477 in Genome Data Viewer
Location:
19p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (2619171..2619465)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (2595434..2595728)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (2619169..2619463)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene G protein subunit gamma 7 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2540747-2541566 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2541567-2542386 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2543207-2544026 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2544027-2544846 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2544847-2545665 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13702 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2546759-2547703 Neighboring gene elongin C pseudogene 28 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2556671-2557284 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2559714-2560214 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13703 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2567191-2567718 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2567719-2568246 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2575316-2575816 Neighboring gene HNF4 motif-containing MPRA enhancer 50 Neighboring gene Sharpr-MPRA regulatory region 4130 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2587299-2588242 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:2592455-2592956 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2603289-2604055 Neighboring gene RNA, 7SL, cytoplasmic 121, pseudogene Neighboring gene H3K4me1 hESC enhancers GRCh37_chr19:2607315-2608169 and GRCh37_chr19:2608170-2609023 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13707 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9803 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13708 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13709 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13710 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr19:2626979-2628178 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13711 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2643435-2643934 Neighboring gene microRNA 7850 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:2650512-2650687 Neighboring gene GNG7 intron CAGE-defined B cell enhancer Neighboring gene MPRA-validated peak3237 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr19:2678080-2678228 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13713 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9804 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13714 Neighboring gene DIRAS family GTPase 1

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_057564.1 

    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    2619171..2619465
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    2595434..2595728
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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