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LOC129929170 ATAC-STARR-seq lymphoblastoid silent region 102 [ Homo sapiens (human) ]

Gene ID: 129929170, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129929170
Gene description
ATAC-STARR-seq lymphoblastoid silent region 102
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 LOC129929170 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 (2044990..2045069)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (1480505..1480584)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (1976429..1976508)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378589 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1949800-1950378 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1950379-1950956 Neighboring gene uncharacterized LOC105378590 Neighboring gene gamma-aminobutyric acid type A receptor subunit delta Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1974620-1975249 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 101 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1977985-1978738 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1978739-1979492 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 103 Neighboring gene PRKCZ divergent transcript Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_1556 Neighboring gene protein kinase C zeta Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:2016670-2017668 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2026419-2026920 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2026921-2027420 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 46 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:2061703-2062652 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:2062653-2063602 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:2064553-2065502 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2068353-2069301 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:2071397-2071980 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:2105285-2105451 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2107005-2107613 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2111308-2112266 Neighboring gene PRKCZ antisense RNA 1

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_162227.1 

    Range
    101..180
    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
    2044990..2045069
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    1480505..1480584
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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