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LOC129929609 ATAC-STARR-seq lymphoblastoid active region 329 [ Homo sapiens (human) ]

Gene ID: 129929609, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129929609
Gene description
ATAC-STARR-seq lymphoblastoid active region 329
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 LOC129929609 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (21343287..21343336)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (21170342..21170391)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (21669780..21669829)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene endothelin converting enzyme 1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:21587933-21589132 Neighboring gene uncharacterized LOC124903872 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:21591626-21592452 Neighboring gene Sharpr-MPRA regulatory region 15718 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21600579-21601078 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21603224-21604202 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:21604203-21605179 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:21610131-21610992 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21615400-21615961 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 377 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 378 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 326 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:21620661-21621860 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21623064-21623668 Neighboring gene ECE1 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21633717-21634404 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21637234-21637788 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:21641652-21642441 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:21643535-21644352 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:21644353-21645170 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:21645989-21646806 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:21648477-21649296 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:21650210-21650770 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:21654133-21654691 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:21655565-21656222 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 328 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21664994-21665936 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 330 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 331 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 379 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 380 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 332 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 333 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21682211-21682712 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21682713-21683212 Neighboring gene protein phosphatase 1 regulatory inhibitor subunit 11 pseudogene 1 Neighboring gene PDE4DIP pseudogene 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_162666.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    21343287..21343336
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    21170342..21170391
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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