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LOC129929783 ATAC-STARR-seq lymphoblastoid active region 465 [ Homo sapiens (human) ]

Gene ID: 129929783, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129929783
Gene description
ATAC-STARR-seq lymphoblastoid active region 465
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 LOC129929783 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 (25775200..25775369)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (25612681..25612850)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (26101691..26101860)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 455 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 457 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 458 Neighboring gene macoilin 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25830121-25830686 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25829553-25830120 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25832992-25833901 Neighboring gene MPRA-validated peak128 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25844344-25844991 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25845160-25845754 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 459 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 456 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 457 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25875990-25876603 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25889735-25890362 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25893282-25894005 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25894006-25894730 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25894731-25895454 Neighboring gene low density lipoprotein receptor adaptor protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25900468-25901335 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25903029-25903950 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25903951-25904872 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25908041-25908889 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25910781-25911344 Neighboring gene Sharpr-MPRA regulatory region 3419 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 460 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 458 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 459 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 461 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25947842-25948342 Neighboring gene MPRA-validated peak129 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 462 Neighboring gene MPRA-validated peak130 silencer Neighboring gene mannosidase alpha class 1C member 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 460 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 463 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:26019008-26019256 Neighboring gene Sharpr-MPRA regulatory region 1026 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:26030010-26030510 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:26030511-26031011 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:26032137-26033112 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:26033113-26034088 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:26034089-26035064 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:26035065-26036040 Neighboring gene MPRA-validated peak132 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:26050687-26051187 Neighboring gene NANOG hESC enhancer GRCh37_chr1:26051273-26051916 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:26074639-26075196 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:26075197-26075754 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:26076313-26076868 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:26078211-26078710 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:26083919-26084418 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:26098327-26099299 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 464 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:26106463-26107085 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:26107086-26107708 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:26110213-26110835 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:26125878-26126599 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:26137118-26137992 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:26144488-26144988 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 462 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 466 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 463 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 467 Neighboring gene selenoprotein N Neighboring gene uncharacterized LOC646471 Neighboring gene mitochondrial fission regulator 1 like

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_162837.1 

    Range
    101..270
    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
    25775200..25775369
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    25612681..25612850
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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