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LOC129931707 ATAC-STARR-seq lymphoblastoid silent region 1461 [ Homo sapiens (human) ]

Gene ID: 129931707, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129931707
Gene description
ATAC-STARR-seq lymphoblastoid silent region 1461
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 LOC129931707 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 (160549438..160549487)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (159686537..159686586)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (160519228..160519277)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371467 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1924 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1925 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1926 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1927 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1928 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:160460168-160461367 Neighboring gene SLAM family member 6 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1929 Neighboring gene uncharacterized LOC105371468 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1930 Neighboring gene Sharpr-MPRA regulatory region 7182 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1931 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1932 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1933 Neighboring gene CD84 molecule Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1934 Neighboring gene NANOG hESC enhancer GRCh37_chr1:160567464-160567965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1935 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1936 Neighboring gene signaling lymphocytic activation molecule family member 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1937 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1938 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1939 Neighboring gene uncharacterized LOC107985220 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1940 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:160621837-160622647 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:160622648-160623458 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1942 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:160635284-160635845 Neighboring gene SET pseudogene 9

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_164750.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    160549438..160549487
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    159686537..159686586
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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