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LOC129929663 ATAC-STARR-seq lymphoblastoid active region 365 [ Homo sapiens (human) ]

Gene ID: 129929663, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129929663
Gene description
ATAC-STARR-seq lymphoblastoid active region 365
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 LOC129929663 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 (23528502..23528631)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (23363068..23363197)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (23854994..23855123)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903875 Neighboring gene ArfGAP with SH3 domain, ankyrin repeat and PH domain 3 Neighboring gene Sharpr-MPRA regulatory region 12987 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:23800831-23801332 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:23801333-23801832 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 412 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 413 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 414 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 364 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:23829854-23830688 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:23830689-23831522 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:23847293-23848492 Neighboring gene uncharacterized LOC101928163 Neighboring gene E2F transcription factor 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:23854779-23854975 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:23857131-23857279 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 415 Neighboring gene Sharpr-MPRA regulatory region 6048 Neighboring gene uncharacterized LOC124903876 Neighboring gene Sharpr-MPRA regulatory region 7496 Neighboring gene uncharacterized LOC105376859 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:23875384-23875934 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 416 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 366 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:23886059-23886305 Neighboring gene inhibitor of DNA binding 3

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_162720.1 

    Range
    101..230
    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
    23528502..23528631
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_014040926.1 Reference GRCh38.p14 PATCHES

    Range
    298481..298610
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    23363068..23363197
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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