U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC123466228 Sharpr-MPRA regulatory region 8435 [ Homo sapiens (human) ]

Gene ID: 123466228, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC123466228
Gene description
Sharpr-MPRA regulatory region 8435
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
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 H3K27ac and H3K4me1 histone modifications. Another subregion was validated as a repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 21:Repr, strong Polycomb repression). [provided by RefSeq, Jan 2023]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
4p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (7806122..7806881)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (7778020..7778779)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (7807849..7808143)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene sortilin related VPS10 domain containing receptor 2 Neighboring gene uncharacterized LOC124900655 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7516537-7517180 Neighboring gene uncharacterized LOC124900654 Neighboring gene Sharpr-MPRA regulatory region 5388 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7541780-7542286 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7572135-7572688 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7572689-7573243 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7594819-7595716 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:7618209-7618398 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:7652905-7653495 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:7654677-7655267 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:7657631-7658221 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7658222-7658811 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7675244-7675744 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7678472-7679464 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7698611-7699152 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7699153-7699695 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:7703459-7704127 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7706967-7707838 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7710414-7710931 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7710932-7711448 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7712713-7713213 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7715853-7716582 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7735941-7736733 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21275 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7747402-7747902 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7754061-7754562 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7754563-7755062 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_chr4:7764789-7765495 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7764080-7764788 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7769393-7770308 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 AFAP1 antisense RNA 1 Neighboring gene uncharacterized LOC124900656 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:7806583-7807151 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:7806013-7806582 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 Sharpr-MPRA regulatory region 14367 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 actin filament associated protein 1 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 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 uncharacterized LOC389199 Neighboring gene actin binding LIM protein family member 2

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

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

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

Go to the top of the page Help

Other Names

  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:7807900-7808608

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_077503.2 

    Range
    101..860
    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    7806122..7806881
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    7778020..7778779
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases