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LOC129934794 ATAC-STARR-seq lymphoblastoid active region 16543 [ Homo sapiens (human) ]

Gene ID: 129934794, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129934794
Gene description
ATAC-STARR-seq lymphoblastoid active region 16543
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 LOC129934794 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 (134020927..134021026)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (134460436..134460535)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (134778498..134778597)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene NCK associated protein 5 Neighboring gene NANOG hESC enhancer GRCh37_chr2:134401501-134402008 Neighboring gene RN7SK pseudogene 93 Neighboring gene Sharpr-MPRA regulatory region 15675 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:134575595-134576794 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16541 Neighboring gene uncharacterized LOC105373627 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16542 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:134742538-134743737 Neighboring gene uncharacterized LOC105373628 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:134821977-134822608 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16544 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:134864951-134865484 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:134866541-134867202 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:134867203-134867862 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11975 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11974 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11972 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11971 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11973 Neighboring gene NANOG hESC enhancer GRCh37_chr2:134891163-134891785 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:134891786-134892407 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_52669 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16545 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:134915432-134916037 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:134916038-134916642 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16546 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_52692 Neighboring gene NANOG hESC enhancer GRCh37_chr2:134960700-134961201 Neighboring gene Sharpr-MPRA regulatory region 5769 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11976 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16547 Neighboring gene microRNA 3679 Neighboring gene alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase Neighboring gene RNA, 5S ribosomal pseudogene 104

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_167810.1 

    Range
    101..200
    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
    134020927..134021026
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    134460436..134460535
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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