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LOC112694698 Sharpr-MPRA regulatory region 2213 [ Homo sapiens (human) ]

Gene ID: 112694698, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112694698
Gene description
Sharpr-MPRA regulatory region 2213
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 both HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 4:PromP, inactive/poised promoter, highly conserved) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 4:PromP). 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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Location:
20p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (3781342..3781747)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (3812282..3812687)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (3761989..3762283)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:3713394-3713973 Neighboring gene heat shock protein family A (Hsp70) member 12B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:3722898-3723425 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:3725082-3725992 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:3729440-3729992 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:3729993-3730543 Neighboring gene adipose secreted signaling protein Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:3747545-3748309 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:3748437-3749023 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17482 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12627 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:3759113-3759730 Neighboring gene sperm flagellar 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:3766083-3766793 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:3766794-3767503 Neighboring gene centromere protein B Neighboring gene cell division cycle 25B Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:3775953-3776684 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12629 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12630 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:3777341-3777548 Neighboring gene Sharpr-MPRA regulatory region 3723 Neighboring gene Sharpr-MPRA regulatory region 8683 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:3782484-3783683

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 17483

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_060728.2 

    Range
    101..506
    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    3781342..3781747
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    3812282..3812687
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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