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LOC129933639 ATAC-STARR-seq lymphoblastoid active region 15689 [ Homo sapiens (human) ]

Gene ID: 129933639, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129933639
Gene description
ATAC-STARR-seq lymphoblastoid active region 15689
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 LOC129933639 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 (45700458..45700507)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (45705496..45705545)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (45927597..45927646)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102724965 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11439 Neighboring gene Sharpr-MPRA regulatory region 4153 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11440 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45878872-45879492 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:45899906-45900117 Neighboring gene PRKCE antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15688 Neighboring gene protein kinase C epsilon Neighboring gene tRNA-Gln (anticodon TTG) 5-1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15690 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15691 Neighboring gene NANOG hESC enhancer GRCh37_chr2:45959936-45960443 Neighboring gene Sharpr-MPRA regulatory region 1594 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:46013490-46014689 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15692 Neighboring gene Sharpr-MPRA regulatory region 10855 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:46050503-46051025 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:46051026-46051547 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15693 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15694 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr2:46063209-46063734 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15695 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11443 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15696 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:46121150-46121322 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15697 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11445 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15698 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:46185885-46186435 Neighboring gene uncharacterized LOC124907761 Neighboring gene Sharpr-MPRA regulatory region 2946 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:46190573-46191772

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_166665.1 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    45700458..45700507
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    45705496..45705545
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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