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LOC112978668 Sharpr-MPRA regulatory region 14367 [ Homo sapiens (human) ]

Gene ID: 112978668, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112978668
Gene description
Sharpr-MPRA regulatory region 14367
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 K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 9:DNaseU, primarily UW DNase, weaker open chromatin sites). [provided by RefSeq, Aug 2018]
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Genomic context

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Location:
4p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (7831402..7831696)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (7803306..7803600)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (7833129..7833423)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr4:7755607-7755833 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7758626-7759126 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7764080-7764788 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7764789-7765495 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7769393-7770308 Neighboring gene AFAP1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21276 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21277 Neighboring gene heart enhancer 19 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21278 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21279 Neighboring gene actin filament associated protein 1 Neighboring gene uncharacterized LOC124900656 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:7806013-7806582 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:7806583-7807151 Neighboring gene Sharpr-MPRA regulatory region 8435 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:7809617-7810117 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr4:7827707-7828208 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr4:7828209-7828708 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:7830049-7830549 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:7845474-7845654 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15253 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7851945-7852446 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7854640-7855140 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7884073-7884574 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:7895735-7895928 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7916363-7917329 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:7919591-7920401 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:7920402-7921211 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:7940549-7941053 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15254 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7951399-7951898 Neighboring gene uncharacterized LOC389199 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7957833-7958334 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7958335-7958834 Neighboring gene Sharpr-MPRA regulatory region 6491 Neighboring gene uncharacterized LOC124900657 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:7973234-7973789 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:7973790-7974346 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15255 Neighboring gene actin binding LIM protein family member 2

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_061523.1 

    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
    7831402..7831696
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    7803306..7803600
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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