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LOC129932979 ATAC-STARR-seq lymphoblastoid active region 15219 [ Homo sapiens (human) ]

Gene ID: 129932979, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129932979
Gene description
ATAC-STARR-seq lymphoblastoid active region 15219
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 LOC129932979 in Genome Data Viewer
Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (884774..884823)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (884246..884295)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (880460..880509)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373480 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:766549-767048 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:776200-776860 Neighboring gene long intergenic non-protein coding RNA 1115 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:816439-816939 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr2:826030-826932 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr2:826933-827834 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:850078-851277 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:863929-865128 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:875979-876480 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:886383-886882 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:905231-905732 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:906278-906778 Neighboring gene long intergenic non-protein coding RNA 1939 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:932826-933706 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11102 Neighboring gene SNTG2 antisense RNA 1 Neighboring gene syntrophin gamma 2

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_166004.1 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    884774..884823
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    884246..884295
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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