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LOC129932983 ATAC-STARR-seq lymphoblastoid silent region 11105 [ Homo sapiens (human) ]

Gene ID: 129932983, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129932983
Gene description
ATAC-STARR-seq lymphoblastoid silent region 11105
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 LOC129932983 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 (2504175..2504224)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (2514428..2514477)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (2507947..2507996)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985838 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:1846879-1847533 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:1847534-1848187 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:1868997-1869620 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:1878441-1878941 Neighboring gene myelin transcription factor 1 like 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_chr2:2029757-2030573 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:2028821-2029320 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11104 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 P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:2530602-2531801 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:2569029-2569986 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:2641129-2641629 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:2650988-2651602 Neighboring gene uncharacterized LOC107985839 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:2660703-2661676 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:2665611-2666112 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:2668465-2669157 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:2700671-2701170 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:2700169-2700670 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:2706918-2707875 Neighboring gene uncharacterized LOC105373390 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15220 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:2775469-2775986 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:2791409-2792013 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:2792014-2792618 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:2792619-2793223 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:2796071-2796790 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:2796791-2797509 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:2841318-2841951

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_166008.1 

    Range
    101..150
    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
    2504175..2504224
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    2514428..2514477
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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