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LOC129932954 ATAC-STARR-seq lymphoblastoid active region 2870 [ Homo sapiens (human) ]

Gene ID: 129932954, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129932954
Gene description
ATAC-STARR-seq lymphoblastoid active region 2870
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 LOC129932954 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 (247440217..247440536)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (246876859..246877178)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (247603519..247603838)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:247499115-247499615 Neighboring gene uncharacterized LOC124904574 Neighboring gene Sharpr-MPRA regulatory region 1744 Neighboring gene ZNF496 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2866 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:247525936-247526480 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2047 Neighboring gene uncharacterized LOC107985375 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:247556143-247556425 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2867 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2868 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:247587345-247587508 Neighboring gene NLR family pyrin domain containing 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2869 Neighboring gene uncharacterized LOC124904575 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2871 Neighboring gene olfactory receptor family 2 subfamily B member 11 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:247634472-247634665 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:247634852-247635484 Neighboring gene olfactory receptor family 2 subfamily W member 5 pseudogene

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_165979.1 

    Range
    101..420
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    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
    247440217..247440536
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791757.1 Reference GRCh38.p14 PATCHES

    Range
    206660..206979
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    246876859..246877178
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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