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LOC112577552 Sharpr-MPRA regulatory region 1224 [ Homo sapiens (human) ]

Gene ID: 112577552, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112577552
Gene description
Sharpr-MPRA regulatory region 1224
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. It was validated as a functional enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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Location:
1q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (230127002..230127296)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (229506584..229506878)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (230262749..230263043)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:230153835-230154406 Neighboring gene long intergenic non-protein coding RNA 1736 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:230155973-230156473 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:230182250-230182750 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230194023-230194523 Neighboring gene U7 small nuclear RNA Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2708 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1936 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1937 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2709 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:230207245-230207425 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:230220010-230220551 Neighboring gene polypeptide N-acetylgalactosaminyltransferase 2 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:230240174-230241373 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2711 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2713 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2712 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:230247432-230248098 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:230248997-230250196 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2714 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2715 Neighboring gene Sharpr-MPRA regulatory region 12256 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230272664-230273164 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230273165-230273665 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:230276043-230276635 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2716 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:230311720-230311947 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:230321452-230322190 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:230322191-230322929 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:230334008-230334701 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230336117-230336616 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230361793-230362294 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230362295-230362794 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:230387089-230387750 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:230387751-230388411 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230390520-230391020 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230391021-230391521 Neighboring gene uncharacterized LOC124904542 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230400862-230401362 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230401363-230401863 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230402952-230403462 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:230403463-230403971 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:230403972-230404481 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:230404482-230404990 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2717 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230422195-230422694 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230423879-230424378 Neighboring gene NANOG hESC enhancer GRCh37_chr1:230431082-230431583 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1939 Neighboring gene putative uncharacterized protein FLJ46204 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230452427-230452928 Neighboring gene piggyBac transposable element derived 5

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. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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

  • ATAC-STARR-seq lymphoblastoid silent region 1938

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_060470.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    230127002..230127296
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    229506584..229506878
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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