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LOC122056800 Sharpr-MPRA regulatory region 1026 [ Homo sapiens (human) ]

Gene ID: 122056800, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122056800
Gene description
Sharpr-MPRA regulatory region 1026
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 H3K4me1 histone modification. 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 HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations). [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
1p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (25695710..25696232)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (25533052..25533574)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (26022429..26022723)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 455 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 457 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 458 Neighboring gene macoilin 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25830121-25830686 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25829553-25830120 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25832992-25833901 Neighboring gene MPRA-validated peak128 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25844344-25844991 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25845160-25845754 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 459 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 456 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 457 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25875990-25876603 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25889735-25890362 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25893282-25894005 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25894006-25894730 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25894731-25895454 Neighboring gene low density lipoprotein receptor adaptor protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25900468-25901335 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25903029-25903950 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25903951-25904872 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25908041-25908889 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25910781-25911344 Neighboring gene Sharpr-MPRA regulatory region 3419 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 460 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 458 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 459 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 461 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25947842-25948342 Neighboring gene MPRA-validated peak129 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 462 Neighboring gene MPRA-validated peak130 silencer Neighboring gene mannosidase alpha class 1C member 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 460 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 463 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:26019008-26019256 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:26030010-26030510 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:26030511-26031011 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:26032137-26033112 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:26033113-26034088 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:26034089-26035064 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:26035065-26036040 Neighboring gene MPRA-validated peak132 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:26050687-26051187 Neighboring gene NANOG hESC enhancer GRCh37_chr1:26051273-26051916 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:26074639-26075196 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:26075197-26075754 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:26076313-26076868 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:26078211-26078710 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:26083919-26084418 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:26098327-26099299 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 464 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 465 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:26106463-26107085 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:26107086-26107708 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:26110213-26110835 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:26125878-26126599 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:26137118-26137992 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:26144488-26144988 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 462 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 466 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 463 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 467 Neighboring gene selenoprotein N Neighboring gene uncharacterized LOC646471 Neighboring gene mitochondrial fission regulator 1 like

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
  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

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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)

General gene information

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Other Names

  • H3K4me1 hESC enhancer GRCh37_chr1:26022201-26022700

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_076256.2 

    Range
    101..623
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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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    25695710..25696232
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    25533052..25533574
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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