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LOC130059904 ATAC-STARR-seq lymphoblastoid silent region 7969 [ Homo sapiens (human) ]

Gene ID: 130059904, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130059904
Gene description
ATAC-STARR-seq lymphoblastoid silent region 7969
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 LOC130059904 in Genome Data Viewer
Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (2049704..2050503)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (1937608..1938407)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (1952998..1953797)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene reticulon 4 receptor like 1 Neighboring gene uncharacterized LOC105371486 Neighboring gene uncharacterized LOC105371485 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11461 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7966 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:1927475-1928020 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1929189-1929689 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:1933787-1934378 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:1933195-1933786 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11462 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7967 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11463 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7968 Neighboring gene uncharacterized LOC124903896 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1954503-1955398 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7970 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7971 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7972 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7973 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7974 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7975 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7976 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7977 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7978 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7979 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:1961456-1961958 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7980 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7981 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7985 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7984 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7983 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11464 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1968405-1969158 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11465 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11466 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:1974493-1975692 Neighboring gene uncharacterized LOC107984988 Neighboring gene diphthamide biosynthesis 1 Neighboring gene OVCA2 serine hydrolase domain containing Neighboring gene microRNA 132 Neighboring gene microRNA 212 Neighboring gene HIC ZBTB transcriptional repressor 1 Neighboring gene SMG6 nonsense mediated mRNA decay factor

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_194325.1 

    Range
    101..900
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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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    2049704..2050503
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    1937608..1938407
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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