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LOC129936957 ATAC-STARR-seq lymphoblastoid active region 20016 [ Homo sapiens (human) ]

Gene ID: 129936957, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129936957
Gene description
ATAC-STARR-seq lymphoblastoid active region 20016
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 an enhancer based on its ability to activate 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 LOC129936957 in Genome Data Viewer
Location:
chromosome: 3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (59444320..59444369)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (59484622..59484671)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (59430046..59430095)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377109 Neighboring gene FAM3 metabolism regulating signaling molecule D Neighboring gene CFAP20 domain containing Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:58792456-58792956 Neighboring gene CFAP20DC antisense RNA 1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:58828169-58828785 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:58859831-58861030 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:58876285-58876824 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:58884619-58885120 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20014 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:58940883-58941482 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:58983704-58984903 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:59017398-59018230 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:59044085-59044335 Neighboring gene CFAP20DC divergent transcript Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:59113978-59114502 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:59114503-59115026 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20015 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14492 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14493 Neighboring gene Sharpr-MPRA regulatory region 3507 Neighboring gene SNRPB2 pseudogene 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:59599597-59599768 Neighboring gene hCG1813818

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_169968.1 

    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    59444320..59444369
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    59484622..59484671
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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