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LOC129933436 ATAC-STARR-seq lymphoblastoid active region 15544 [ Homo sapiens (human) ]

Gene ID: 129933436, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129933436
Gene description
ATAC-STARR-seq lymphoblastoid active region 15544
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 LOC129933436 in Genome Data Viewer
Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (30436913..30436992)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (30481248..30481327)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (30659779..30659858)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15536 Neighboring gene uncharacterized LOC102723594 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15537 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:30517185-30517355 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:30523745-30524427 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:30524428-30525109 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:30525110-30525792 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:30525793-30526473 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15538 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15539 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15540 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15541 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15542 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15543 Neighboring gene long intergenic non-protein coding RNA 1936 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:30633050-30633962 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:30666124-30666624 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:30669802-30670539 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:30670540-30671276 Neighboring gene lysocardiolipin acyltransferase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:30738762-30739262 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:30739263-30739763 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:30835819-30836816 Neighboring gene MPRA-validated peak3643 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15548 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr2:30874941-30875672 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:30875673-30876403 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11329 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:30943850-30944350 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:30944351-30944851 Neighboring gene calpain 13 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:30988245-30988745 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:31020137-31020846 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:31020847-31021554

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_166461.1 

    Range
    101..180
    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    30436913..30436992
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    30481248..30481327
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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