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LOC129936340 ATAC-STARR-seq lymphoblastoid active region 19578 [ Homo sapiens (human) ]

Gene ID: 129936340, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129936340
Gene description
ATAC-STARR-seq lymphoblastoid active region 19578
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 LOC129936340 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 (19947686..19947735)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (19951831..19951880)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (19989178..19989227)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376984 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_67588 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:19896761-19897348 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:19906013-19907212 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_67669 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_67675 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_67680 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_67685 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_67687 and experimental_67689 Neighboring gene EF-hand domain family member B Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_67692 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_67694 Neighboring gene Sharpr-MPRA regulatory region 12217 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:19987470-19988071 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_67714 and experimental_67716 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:19989274-19989873 Neighboring gene heat shock protein family A (Hsp70) member 8 pseudogene 18 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_67724 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_67730 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_67732 Neighboring gene RAB5A, member RAS oncogene family Neighboring gene ReSE screen-validated silencer GRCh37_chr3:20044283-20044424 Neighboring gene uncharacterized LOC124909352 Neighboring gene protein phosphatase 2C like domain containing 1 Neighboring gene RNA, U4 small nuclear 85, pseudogene Neighboring gene SAP18 pseudogene 3

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_169351.1 

    Range
    101..150
    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
    19947686..19947735
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    19951831..19951880
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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