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LOC112694764 Sharpr-MPRA regulatory region 10527 [ Homo sapiens (human) ]

Gene ID: 112694764, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112694764
Gene description
Sharpr-MPRA regulatory region 10527
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 25:Art, potential CNV or repetitive artifacts), with weak activation in HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jul 2018]
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Genomic context

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Location:
22q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (19947746..19948040)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (20325435..20325729)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (19935269..19935563)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene thioredoxin reductase 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19878079-19878587 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19878588-19879096 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19879097-19879604 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19879605-19880113 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:19880414-19880618 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19883730-19884368 Neighboring gene ribosomal protein L8 pseudogene 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19889902-19890838 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr22:19894389-19895588 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19904338-19904948 Neighboring gene endogenous retrovirus group K member 24 Gag polyprotein-like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19927919-19928489 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19928490-19929059 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13467 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13468 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13469 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18664 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18665 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19931341-19931910 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19931911-19932479 Neighboring gene Sharpr-MPRA regulatory region 2516 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19940787-19941410 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19941411-19942032 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19942297-19942948 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:19943251-19943418 Neighboring gene catechol-O-methyltransferase Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19949617-19950332 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19950333-19951048 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19951049-19951764 Neighboring gene microRNA 4761 Neighboring gene ARVCF delta catenin family member Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19970318-19971255 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19971256-19972192 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19973130-19974065 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13470 Neighboring gene uncharacterized LOC124905082

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_060847.1 

    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    19947746..19948040
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    20325435..20325729
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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