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LOC130059041 ATAC-STARR-seq lymphoblastoid silent region 7507 [ Homo sapiens (human) ]

Gene ID: 130059041, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130059041
Gene description
ATAC-STARR-seq lymphoblastoid silent region 7507
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 LOC130059041 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 (56424886..56425945)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (62219945..62221016)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (56458798..56459857)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:56226034-56226607 Neighboring gene GNAO1 antisense RNA 1 Neighboring gene G protein subunit alpha o1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:56297649-56298217 Neighboring gene microRNA 3935 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:56311207-56311706 Neighboring gene Sharpr-MPRA regulatory region 182 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:56316059-56316608 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:56316609-56317156 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:56318360-56318881 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:56322213-56322875 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_43505 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:56337209-56337709 Neighboring gene NANOG hESC enhancer GRCh37_chr16:56339811-56340312 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:56346109-56347085 Neighboring gene Sharpr-MPRA regulatory region 3823 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:56379271-56379958 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:56382339-56382839 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:56389828-56389987 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10848 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:56396251-56396424 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:56396447-56396947 Neighboring gene autocrine motility factor receptor Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10849 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10850 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7508 Neighboring gene nudix hydrolase 21 Neighboring gene 2-oxoglutarate and iron dependent oxygenase domain containing 1 Neighboring gene Bardet-Biedl syndrome 2

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_193462.1 

    Range
    101..1160
    Download
    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
    56424886..56425945
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    62219945..62221016
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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