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LOC130059500 ATAC-STARR-seq lymphoblastoid silent region 7755 [ Homo sapiens (human) ]

Gene ID: 130059500, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130059500
Gene description
ATAC-STARR-seq lymphoblastoid silent region 7755
Gene type
biological region
Feature type(s)
regulatory: 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 represents an accessible chromatin region 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) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC130059500 in Genome Data Viewer
Location:
chromosome: 16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (81315569..81315838)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (87376335..87376604)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (81349174..81349443)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81150474-81151032 Neighboring gene RNA, U6 small nuclear 1191, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81171151-81171768 Neighboring gene Sharpr-MPRA regulatory region 3111 Neighboring gene polycystin 1 like 2 (gene/pseudogene) Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:81191716-81192216 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:81246022-81246522 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:81255488-81255706 Neighboring gene beta-carotene oxygenase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11178 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7754 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7753 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:81420479-81420673 Neighboring gene gigaxonin Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81430852-81431402 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81431403-81431953 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11179 Neighboring gene Sharpr-MPRA regulatory region 12949 Neighboring gene microRNA 4720 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81466113-81467024 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81467025-81467934 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81477254-81477786 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7756 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7757 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7758 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81479951-81480716 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81480717-81481480 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7759 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81482247-81483010 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11182 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81489297-81489981 Neighboring gene Sharpr-MPRA regulatory region 2768 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81491353-81492038 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81497377-81497916 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:81503436-81503936 Neighboring gene c-Maf inducing protein Neighboring gene peptidylprolyl isomerase A pseudogene 51

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. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. 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)

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_193921.1 

    Range
    101..370
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    81315569..81315838
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    87376335..87376604
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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