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LOC130057635 ATAC-STARR-seq lymphoblastoid active region 9874 [ Homo sapiens (human) ]

Gene ID: 130057635, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130057635
Gene description
ATAC-STARR-seq lymphoblastoid active region 9874
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 LOC130057635 in Genome Data Viewer
Location:
chromosome: 15
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (76181577..76181626)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (74052472..74052521)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (76473918..76473967)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene transmembrane protein 266 Neighboring gene uncharacterized LOC124903531 Neighboring gene Sharpr-MPRA regulatory region 3592 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:76432149-76432982 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:76442422-76442685 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:76442959-76443537 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9873 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:76444006-76444636 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:76453363-76454200 Neighboring gene uncharacterized LOC101929439 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9875 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:76482438-76482591 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9876 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:76488419-76488980 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:76488981-76489540 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:76489541-76490100 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:76491300-76491944 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:76491945-76492588 Neighboring gene NANOG hESC enhancer GRCh37_chr15:76526655-76527344 Neighboring gene electron transfer flavoprotein subunit alpha Neighboring gene TYRO3P protein tyrosine kinase pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:76603062-76603562 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:76603563-76604063 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9877 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9878 Neighboring gene CRISPRi-validated cis-regulatory element chr15.2471 Neighboring gene Sharpr-MPRA regulatory region 228 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:76629623-76630434 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9880 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9881 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:76632479-76633234 Neighboring gene uncharacterized LOC124903532 Neighboring gene ISL LIM homeobox 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_192056.1 

    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    76181577..76181626
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    74052472..74052521
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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