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LOC130002172 ATAC-STARR-seq lymphoblastoid active region 28659 [ Homo sapiens (human) ]

Gene ID: 130002172, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130002172
Gene description
ATAC-STARR-seq lymphoblastoid active region 28659
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 LOC130002172 in Genome Data Viewer
Location:
chromosome: 9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (97367256..97367425)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (109539214..109539383)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (100129538..100129707)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene SUGT1P4-STRA6LP-CCDC180 readthrough Neighboring gene SUGT1P4-STRA6LP readthrough Neighboring gene ReSE screen-validated silencer GRCh37_chr9:100057407-100057584 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20098 Neighboring gene Sharpr-MPRA regulatory region 563 Neighboring gene STRA6 like, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100074371-100074871 Neighboring gene coiled-coil domain containing 180 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28658 Neighboring gene microRNA 1302-8 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100148028-100148534 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100148535-100149040 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:100150291-100150855 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28660 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28661 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:100161577-100161764 Neighboring gene uncharacterized LOC286359 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr9:100174359-100174860 and GRCh37_chr9:100174861-100175360 Neighboring gene tudor domain containing 7 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:100226535-100227734 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28663

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_181618.1 

    Range
    101..270
    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    97367256..97367425
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    109539214..109539383
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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