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LOC112533666 Sharpr-MPRA regulatory region 4436 [ Homo sapiens (human) ]

Gene ID: 112533666, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112533666
Gene description
Sharpr-MPRA regulatory region 4436
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. A subregion 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 DNase matched - State 5:Enh, candidate strong enhancer, open chromatin), with weaker activation in HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 14:Gen5', transcription transition, highly expressed genes towards 5' end). This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate 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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See LOC112533666 in Genome Data Viewer
Location:
17q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (73291436..73291784)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (74181216..74181564)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (71287629..71287923)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12691 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:71227250-71228026 Neighboring gene component of oligomeric golgi complex 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12692 Neighboring gene VCP nuclear cofactor family member 1 Neighboring gene mitochondrial nucleoid associated protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12693 Neighboring gene cleavage and polyadenylation specific factor 4 like Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12694 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71280886-71281442 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71281998-71282553 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71282554-71283108 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12695 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71287907-71288788 Neighboring gene CDC42 effector protein 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8922 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8923 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8924 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8925 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71314086-71314838 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71332871-71333770 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71343461-71344310 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71348097-71348598 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71348599-71349098 Neighboring gene Sharpr-MPRA regulatory region 1327 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71357197-71357868 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71359686-71360661 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71361126-71361628 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71375179-71375680 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71376229-71376730 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71376731-71377230 Neighboring gene sidekick cell adhesion molecule 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71396825-71397329 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71397330-71397833 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12698 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71434193-71434693 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12699 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_47326 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71487500-71488358 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71488359-71489217 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71501870-71502807 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71503745-71504682 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71507033-71507902 Neighboring gene uncharacterized LOC101928251 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71530725-71531437 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71533005-71533777 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71536899-71537463 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71542356-71542892 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71544460-71544960 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71544961-71545461 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71556405-71557010 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71557011-71557617 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71560304-71560804 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:71561780-71562370 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr17:71562371-71562960 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71563551-71564139 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71584531-71585034 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71585035-71585539 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr17:71585540-71586043 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr17:71586044-71586548 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71591289-71591834 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71608178-71608714 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71621555-71622080 Neighboring gene uncharacterized LOC124904054

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 active region 12696

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_057294.2 

    Range
    101..449
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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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    73291436..73291784
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    74181216..74181564
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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