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LOC130002639 ATAC-STARR-seq lymphoblastoid active region 29034 [ Homo sapiens (human) ]

Gene ID: 130002639, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130002639
Gene description
ATAC-STARR-seq lymphoblastoid active region 29034
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 LOC130002639 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 (127189208..127189267)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (139395631..139395690)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (129951487..129951546)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene Ral GEF with PH domain and SH3 binding motif 1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:129874135-129874746 Neighboring gene angiopoietin like 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129884227-129884860 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:129884861-129885494 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:129885495-129886128 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29032 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr9:129920824-129922023 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:129928436-129929635 Neighboring gene uncharacterized LOC105376278 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129943177-129943676 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129946409-129946979 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129948384-129948884 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129957118-129957618 Neighboring gene Sharpr-MPRA regulatory region 1494 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29035 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:129961533-129962521 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129969788-129970288 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129970289-129970789 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:129972323-129972840 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:129974395-129974912 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129978722-129979222 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129979223-129979723 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:129981929-129982488 Neighboring gene uncharacterized LOC124902273 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129985710-129986210 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129986211-129986711 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20299 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20300 Neighboring gene uncharacterized LOC124902274 Neighboring gene GTPase activating Rap/RanGAP domain like 3

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_182085.1 

    Range
    101..160
    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
    127189208..127189267
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    139395631..139395690
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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