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LOC129931856 ATAC-STARR-seq lymphoblastoid silent region 1530 [ Homo sapiens (human) ]

Gene ID: 129931856, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129931856
Gene description
ATAC-STARR-seq lymphoblastoid silent region 1530
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 LOC129931856 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (167553451..167553900)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (166904906..166905355)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (167522688..167523137)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101928512 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1526 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1527 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1528 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1529 Neighboring gene CD247 molecule Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:167455187-167455767 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:167472740-167473240 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:167486398-167487597 Neighboring gene uncharacterized LOC107985224 Neighboring gene aldo-keto reductase family 1 member D1 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:167509239-167509739 Neighboring gene GATA motif-containing MPRA enhancer 235 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:167533326-167534525 Neighboring gene cellular repressor of E1A stimulated genes 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2042 Neighboring gene ribosomal protein S18 pseudogene 4 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:167586581-167587780 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2043 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2045 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2044 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1531 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1532 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2046 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:167604143-167604666 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:167604667-167605189 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2047 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:167625876-167626070 Neighboring gene RCSD domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2048 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2049 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:167649515-167649718 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2050 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:167658487-167659686 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:167666863-167667545 Neighboring gene Sharpr-MPRA regulatory region 8181 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2051

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 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_164899.1 

    Range
    101..550
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    167553451..167553900
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    166904906..166905355
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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