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LOC130002982 ATAC-STARR-seq lymphoblastoid active region 29294 [ Homo sapiens (human) ]

Gene ID: 130002982, updated on 14-Oct-2023

Summary

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Gene symbol
LOC130002982
Gene description
ATAC-STARR-seq lymphoblastoid active region 29294
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 LOC130002982 in Genome Data Viewer
Location:
chromosome: 9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (135926911..135926960)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (148154333..148154382)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr9:138712950-138713111 Neighboring gene calmodulin regulated spectrin associated protein 1 Neighboring gene Sharpr-MPRA regulatory region 6734 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:138770145-138770777 Neighboring gene Sharpr-MPRA regulatory region 8889 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:138780903-138781606 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr9:138796685-138797884 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20489 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20490 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20491 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20492 Neighboring gene CAMSAP1 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29293 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:138823557-138824056 Neighboring gene Sharpr-MPRA regulatory region 7357 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:138838500-138839699 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:138842180-138842463 Neighboring gene UBA domain containing 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:138852839-138853339 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:138860297-138860930 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:138863893-138864078 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:138865698-138866480 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:138881416-138882094 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:138882772-138883449 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:138884127-138884804 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:138884805-138885482 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:138904343-138905133 Neighboring gene uncharacterized LOC124902307 Neighboring gene NACC family member 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 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_182428.1 

    Range
    101..150
    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    135926911..135926960
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    148154333..148154382
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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