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LOC129932982 ATAC-STARR-seq lymphoblastoid silent region 11104 [ Homo sapiens (human) ]

Gene ID: 129932982, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129932982
Gene description
ATAC-STARR-seq lymphoblastoid silent region 11104
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 LOC129932982 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 (2120909..2120998)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (2131051..2131140)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (2124681..2124770)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124905967 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:1829865-1830422 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:1842467-1842968 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:1845570-1846224 Neighboring gene uncharacterized LOC107985838 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:1846879-1847533 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:1847534-1848187 Neighboring gene myelin transcription factor 1 like Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:1868997-1869620 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:1878441-1878941 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:1969195-1969716 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:1977845-1978345 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:1990006-1990664 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr2:1990665-1991322 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:2010989-2011490 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:2011491-2011992 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:2028319-2028820 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:2028821-2029320 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:2029757-2030573 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:2149801-2150324 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:2150847-2151369 Neighboring gene NANOG hESC enhancer GRCh37_chr2:2252484-2253019 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:2276633-2277264 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:2295761-2296549 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:2297557-2298056 Neighboring gene MYT1L antisense RNA 1 Neighboring gene uncharacterized LOC105373389 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11105

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_166007.1 

    Range
    101..190
    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    2120909..2120998
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    2131051..2131140
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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