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LOC129937471 ATAC-STARR-seq lymphoblastoid active region 20447 [ Homo sapiens (human) ]

Gene ID: 129937471, updated on 14-Oct-2023

Summary

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Gene symbol
LOC129937471
Gene description
ATAC-STARR-seq lymphoblastoid active region 20447
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 LOC129937471 in Genome Data Viewer
Location:
chromosome: 3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (126982181..126982510)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (129714361..129714690)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:126397718-126398324 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20441 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126423783-126424334 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14680 Neighboring gene SF3A2 pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:126465189-126465888 Neighboring gene coiled-coil-helix-coiled-coil-helix domain containing 6 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:126469383-126470020 Neighboring gene Sharpr-MPRA regulatory regions 1012 and 11425 Neighboring gene regulator of chromosome condensation 2 pseudogene 4 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:126549126-126549983 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:126549984-126550840 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:126570363-126570924 Neighboring gene Sharpr-MPRA regulatory region 387 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:126627623-126627935 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:126629966-126631165 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20445 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:126678753-126679300 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126680398-126680946 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126680947-126681493 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20446 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14681 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14682 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14683 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126713795-126714428 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:126716329-126716962 Neighboring gene Sharpr-MPRA regulatory region 11201 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:126719495-126720128 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20449 Neighboring gene Sharpr-MPRA regulatory region 421 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20450 Neighboring gene plexin A1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:126762997-126763640 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126772262-126772762 Neighboring gene MPRA-validated peak4817 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126783715-126784214 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126789374-126789874 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126789875-126790375 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14684 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126807100-126807726 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126807727-126808352 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126811845-126812457 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126815371-126816008 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126826424-126826924 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126857595-126858095 Neighboring gene MPRA-validated peak4818 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126903541-126904408 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126915318-126916262 Neighboring gene PRR23 family member E

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 across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. 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

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_170481.1 

    Range
    101..430
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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
    126982181..126982510
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    129714361..129714690
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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