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LOC121967046 Sharpr-MPRA regulatory region 14484 [ Homo sapiens (human) ]

Gene ID: 121967046, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121967046
Gene description
Sharpr-MPRA regulatory region 14484
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. A subregion was validated as a functional 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 1:Tss, active promoter, TSS/CpG island region). 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:
1p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (1782770..1783154)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (1217148..1217532)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (1714209..1714503)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ribosomal protein S7 pseudogene Neighboring gene solute carrier family 35 member E2A (pseudogene) Neighboring gene uncharacterized LOC112268218 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 89 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1684563-1685092 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1691433-1692390 Neighboring gene NAD kinase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1705547-1706048 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 90 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 33 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 34 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 35 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 36 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:1721473-1721656 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 38 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 91 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 39 Neighboring gene G protein subunit beta 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1757447-1758350 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 40 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 41 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1782535-1783035 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1783210-1784022 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 44 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 43 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 42 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:1798007-1798184 Neighboring gene Sharpr-MPRA regulatory region 3728 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1820039-1820538 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 92 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 93 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 94 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 95 Neighboring gene GNB1 divergent transcript

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 37

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_076186.2 

    Range
    101..485
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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
    1782770..1783154
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    1217148..1217532
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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