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LOC129935960 ATAC-STARR-seq lymphoblastoid silent region 12504 [ Homo sapiens (human) ]

Gene ID: 129935960, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129935960
Gene description
ATAC-STARR-seq lymphoblastoid silent region 12504
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 LOC129935960 in Genome Data Viewer
Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (239751811..239751880)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (240244454..240244523)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (240673505..240673574)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2991 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:240565957-240566484 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:240566485-240567010 Neighboring gene uncharacterized LOC105373966 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:240582179-240582678 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:240644837-240645402 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:240645403-240645968 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:240667929-240669128 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:240671487-240672397 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:240674643-240675212 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:240678616-240679552 Neighboring gene uncharacterized LOC150935 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:240739699-240740285 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:240741003-240741503 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:240753063-240753578 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:240835310-240835810 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:240835811-240836311 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:240842953-240843860 Neighboring gene NADH:ubiquinone oxidoreductase subunit A10 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:240868321-240868542 Neighboring gene microRNA 4786

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_168971.1 

    Range
    101..170
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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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    239751811..239751880
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_011332689.1 Reference GRCh38.p14 PATCHES

    Range
    54908..54977
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    240244454..240244523
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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