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LOC129999331 ATAC-STARR-seq lymphoblastoid active region 26640 [ Homo sapiens (human) ]

Gene ID: 129999331, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129999331
Gene description
ATAC-STARR-seq lymphoblastoid active region 26640
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 LOC129999331 in Genome Data Viewer
Location:
chromosome: 7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (130012378..130012537)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (131325727..131325886)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (129652218..129652377)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:129416778-129417624 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18633 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18634 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:129420163-129421008 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:129421855-129422700 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:129422701-129423545 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:129424259-129424770 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:129424771-129425281 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26633 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26634 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr7:129426816-129427326 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:129427327-129427837 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:129427838-129428347 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:129432262-129432762 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:129439452-129440063 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:129442015-129442516 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:129442517-129443016 Neighboring gene microRNA 183 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18636 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18637 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18638 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26635 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:129474501-129475160 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr7:129475895-129476430 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:129478138-129479337 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:129482500-129483326 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:129483327-129484153 Neighboring gene ubiquitin conjugating enzyme E2 H Neighboring gene NANOG hESC enhancer GRCh37_chr7:129519616-129520117 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26636 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:129585761-129586260 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:129588587-129589160 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:129589161-129589732 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26637 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18639 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18640 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:129606459-129606647 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:129608210-129608852 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:129608853-129609494 Neighboring gene UBE2H divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18641 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:129630785-129631284 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:129646338-129646838 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:129646839-129647339 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26638 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26639 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:129649077-129650276 Neighboring gene RNA, 5S ribosomal pseudogene 245 Neighboring gene zinc finger C3HC-type containing 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:129690548-129691340 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26642 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26643 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26644 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18642 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26645 Neighboring gene kelch domain containing 10

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_178777.1 

    Range
    101..260
    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    130012378..130012537
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    131325727..131325886
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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