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LOC129932605 ATAC-STARR-seq lymphoblastoid active region 2625 [ Homo sapiens (human) ]

Gene ID: 129932605, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129932605
Gene description
ATAC-STARR-seq lymphoblastoid active region 2625
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 LOC129932605 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 (225467475..225467734)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (224655754..224656013)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (225655177..225655436)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene dynein axonemal heavy chain 14 Neighboring gene uncharacterized LOC124904525 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_5491 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:225614150-225614822 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:225614823-225615494 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2620 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2621 Neighboring gene CRISPRi-validated cis-regulatory element chr1.11936 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2622 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:225633853-225634413 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:225634414-225634974 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:225634975-225635534 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:225643575-225644075 Neighboring gene Sharpr-MPRA regulatory region 13241 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:225648195-225648876 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:225653249-225654138 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2624 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2626 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:225660151-225660670 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:225660671-225661190 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1857 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2627 Neighboring gene uncharacterized LOC124904526 Neighboring gene long intergenic non-protein coding RNA 2765 Neighboring gene lamin B receptor Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:225696090-225697289 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:225705151-225705671 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:225704628-225705150 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:225706601-225707102 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:225736695-225737194 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:225749625-225750126 Neighboring gene ENAH actin regulator Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_5624 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:225802428-225803258 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1858 Neighboring gene uncharacterized LOC102723834 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:225887458-225888657 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:225897976-225899175 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:225900316-225900482

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_165630.1 

    Range
    101..360
    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
    225467475..225467734
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    224655754..224656013
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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