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LOC129929722 ATAC-STARR-seq lymphoblastoid active region 408 [ Homo sapiens (human) ]

Gene ID: 129929722, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129929722
Gene description
ATAC-STARR-seq lymphoblastoid active region 408
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 LOC129929722 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 (24900581..24900630)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (24736302..24736351)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (25227072..25227121)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene chloride intracellular channel 4 Neighboring gene RNA, U6 small nuclear 1208, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25173940-25174664 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 440 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 441 Neighboring gene uncharacterized LOC105376876 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:25192786-25193985 Neighboring gene MPRA-validated peak122 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 406 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 407 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 409 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 410 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 411 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25240971-25241486 Neighboring gene RUNX family transcription factor 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 412 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25254973-25255707 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25255708-25256441 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 443 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25257881-25258470 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 444 Neighboring gene microRNA 6731 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 445 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25264973-25265472 Neighboring gene RUNX3 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 414 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25276177-25276700 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25276701-25277226 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 415 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 446 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:25281264-25282463 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 419 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 420 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 421 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 447 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 422 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 423

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_162778.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    24900581..24900630
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    24736302..24736351
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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