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LOC129938295 ATAC-STARR-seq lymphoblastoid active region 21096 [ Homo sapiens (human) ]

Gene ID: 129938295, updated on 14-Oct-2023

Summary

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Gene symbol
LOC129938295
Gene description
ATAC-STARR-seq lymphoblastoid active region 21096
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 LOC129938295 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 (196620214..196620283)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (199339473..199339542)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:196289997-196291196 Neighboring gene WD repeat domain 53 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:196293567-196294766 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15067 Neighboring gene Sharpr-MPRA regulatory region 4041 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:196296784-196297332 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:196297333-196297880 Neighboring gene F-box protein 45 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:196359126-196359880 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:196361941-196362478 Neighboring gene long intergenic non-protein coding RNA 1063 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15069 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15070 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21097 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21098 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21099 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21100 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21101 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:196374559-196375324 Neighboring gene negative regulator of reactive oxygen species Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:196377623-196378388 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:196386545-196387120

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_171305.1 

    Range
    101..170
    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
    196620214..196620283
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    199339473..199339542
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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