U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC129936310 ATAC-STARR-seq lymphoblastoid active region 19554 [ Homo sapiens (human) ]

Gene ID: 129936310, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC129936310
Gene description
ATAC-STARR-seq lymphoblastoid active region 19554
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]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC129936310 in Genome Data Viewer
Location:
chromosome: 3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (16820597..16820776)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (16821826..16822005)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (16862100..16862279)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene deleted in azoospermia like Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:16699444-16700249 Neighboring gene Sharpr-MPRA regulatory region 448 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:16712625-16713593 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:16717988-16718488 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:16718489-16718989 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:16728537-16729494 Neighboring gene chromodomain Y-like protein Neighboring gene NANOG hESC enhancer GRCh37_chr3:16738083-16738584 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19553 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:16739803-16740450 Neighboring gene CDYL pseudogene 1 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:16791041-16791542 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:16810328-16810902 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr3:16830630-16831603 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19555 Neighboring gene uncharacterized LOC105376972 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:16924592-16925300 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14120 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:16926303-16926804 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:16926805-16927304 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19556 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19557 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14122 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19558 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19559 Neighboring gene phospholipase C like 2 Neighboring gene microRNA 3714

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

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

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See Variation Viewer (GRCh37.p13)

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_169321.1 

    Range
    101..280
    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    16820597..16820776
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_017363813.1 Reference GRCh38.p14 PATCHES

    Range
    133082..133261
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    16821826..16822005
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases