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LOC130064179 ATAC-STARR-seq lymphoblastoid active region 14444 [ Homo sapiens (human) ]

Gene ID: 130064179, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130064179
Gene description
ATAC-STARR-seq lymphoblastoid active region 14444
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 LOC130064179 in Genome Data Viewer
Location:
chromosome: 19
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (33197544..33197603)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (35716181..35716240)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (33688450..33688509)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene WD repeat domain 88 Neighboring gene uncharacterized LOC124904691 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14440 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_51151 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:33666856-33667620 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10491 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10492 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14442 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14443 Neighboring gene tRNA-Thr (anticodon AGT) 1-3 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_51171 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_51179 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_51187 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_51194 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33698023-33698524 Neighboring gene LDL receptor related protein 3 Neighboring gene solute carrier family 7 member 10 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:33723689-33723856 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_51216 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14445 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10493 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33739547-33740048 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10494 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33741253-33742136 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33742137-33743019 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33764565-33765125 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:33765149-33765716 Neighboring gene HNF1 motif-containing MPRA enhancer 13 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33769447-33770004 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33777434-33778421 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:33782467-33783050 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33784308-33785258 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10495 Neighboring gene CCAAT enhancer binding protein alpha

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_198596.1 

    Range
    101..160
    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    33197544..33197603
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    35716181..35716240
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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