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LOC130061972 ATAC-STARR-seq lymphoblastoid active region 12979 [ Homo sapiens (human) ]

Gene ID: 130061972, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130061972
Gene description
ATAC-STARR-seq lymphoblastoid active region 12979
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 LOC130061972 in Genome Data Viewer
Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (81865445..81865494)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (82732610..82732659)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (79823321..79823370)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79791171-79791684 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79792198-79792710 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79792711-79793223 Neighboring gene protein phosphatase 1 regulatory subunit 27 Neighboring gene prolyl 4-hydroxylase subunit beta Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:79813353-79813852 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9153 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9154 Neighboring gene uncharacterized LOC124904086 Neighboring gene Sharpr-MPRA regulatory region 9355 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79823980-79824608 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79825239-79825867 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79825868-79826497 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79826498-79827126 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9158 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12981 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9159 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9160 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12982 Neighboring gene Rho GDP dissociation inhibitor alpha Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12983 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:79846281-79847480 Neighboring gene Aly/REF export factor Neighboring gene anaphase promoting complex subunit 11

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_197061.1 

    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    81865445..81865494
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    82732610..82732659
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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