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LOC129995978 ATAC-STARR-seq lymphoblastoid silent region 16989 [ Homo sapiens (human) ]

Gene ID: 129995978, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129995978
Gene description
ATAC-STARR-seq lymphoblastoid silent region 16989
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 LOC129995978 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (24494975..24495364)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (24364956..24365345)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (24495203..24495592)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene doublecortin domain containing 2 Neighboring gene RNA, U6 small nuclear 391, pseudogene Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:24400121-24400856 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:24400857-24401592 Neighboring gene Sharpr-MPRA regulatory region 326 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:24403801-24404535 Neighboring gene magnesium transporter MRS2 Neighboring gene MPRA-validated peak5733 silencer Neighboring gene glycosylphosphatidylinositol specific phospholipase D1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16990 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24152 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24153 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16991 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16992 Neighboring gene aldehyde dehydrogenase 5 family member A1 Neighboring gene uncharacterized LOC124901277 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:24538795-24539994 Neighboring gene NANOG hESC enhancer GRCh37_chr6:24547459-24547981 Neighboring gene KIAA0319 Neighboring gene MPRA-validated peak5735 silencer Neighboring gene keratin 8 pseudogene 43

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_175424.1 

    Range
    101..490
    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    24494975..24495364
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    24364956..24365345
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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