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LOC130059531 ATAC-STARR-seq lymphoblastoid active region 11209 [ Homo sapiens (human) ]

Gene ID: 130059531, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130059531
Gene description
ATAC-STARR-seq lymphoblastoid active region 11209
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 LOC130059531 in Genome Data Viewer
Location:
chromosome: 16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (81808286..81808395)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (87872124..87872233)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (81841891..81842000)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene c-Maf inducing protein Neighboring gene uncharacterized LOC100129617 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:81716567-81717362 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:81719349-81720088 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:81720089-81720826 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81724705-81725344 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:81738285-81738786 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:81745144-81745826 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:81746509-81747190 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:81747191-81747871 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:81750745-81750968 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11197 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11198 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11199 Neighboring gene Sharpr-MPRA regulatory region 4528 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:81758203-81758451 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:81770025-81770957 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11200 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81772148-81772930 Neighboring gene uncharacterized LOC105369213 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81779157-81779776 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:81780739-81780931 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11203 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81785671-81786279 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81786280-81786887 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11204 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7763 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7762 Neighboring gene Sharpr-MPRA regulatory region 4151 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7761 Neighboring gene Sharpr-MPRA regulatory region 14941 Neighboring gene phospholipase C gamma 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11205 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11206 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11207 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11208 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11210 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11211 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11212 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11213 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11214 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11215 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11216 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11217 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11218 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11219 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11220 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11221 Neighboring gene uncharacterized LOC124903731 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81864849-81865430 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81865431-81866012 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11222 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11223 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11224 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:81933783-81934284 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:81946417-81946916 Neighboring gene RN7SK pseudogene 176

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_193952.1 

    Range
    101..210
    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    81808286..81808395
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    87872124..87872233
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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