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LOC130062136 ATAC-STARR-seq lymphoblastoid active region 13062 [ Homo sapiens (human) ]

Gene ID: 130062136, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130062136
Gene description
ATAC-STARR-seq lymphoblastoid active region 13062
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 LOC130062136 in Genome Data Viewer
Location:
chromosome: 18
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (8610675..8610724)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (8773842..8773891)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (8610673..8610722)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr18:8521740-8522939 Neighboring gene thymocyte selection associated family member 3, pseudogene Neighboring gene aldo-keto reductase family 1 member B1 pseudogene 6 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9271 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9272 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:8614551-8615372 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:8618188-8618688 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:8618689-8619189 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr18:8621915-8622568 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr18:8622569-8623221 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:8623222-8623874 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:8623875-8624527 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:8630542-8631102 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr18:8635328-8636527 Neighboring gene RAB12, member RAS oncogene family Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:8646400-8647022 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:8647023-8647645 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:8657881-8658380 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:8659695-8660294 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:8662265-8662849 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:8690155-8691020 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9273 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9274 Neighboring gene TOMM20 pseudogene 3 Neighboring gene gastric cancer associated transcript 2 Neighboring gene microtubule crosslinking factor 1

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_197201.1 

    Range
    101..150
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    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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    8610675..8610724
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    8773842..8773891
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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