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LOC130059616 ATAC-STARR-seq lymphoblastoid active region 11266 [ Homo sapiens (human) ]

Gene ID: 130059616, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130059616
Gene description
ATAC-STARR-seq lymphoblastoid active region 11266
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 LOC130059616 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 (85227179..85227288)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (91293339..91293448)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (85260785..85260894)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371382 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85180218-85180762 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85180763-85181307 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7800 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7801 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11264 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85187102-85187602 Neighboring gene long intergenic non-protein coding RNA 2139 Neighboring gene Sharpr-MPRA regulatory region 15454 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:85205301-85206012 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:85204591-85205300 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:85221161-85222101 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85224026-85224526 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:85233339-85234538 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:85234576-85235312 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:85240619-85241362 Neighboring gene Sharpr-MPRA regulatory region 3131 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85248283-85248783 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:85254771-85255472 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85255473-85256172 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11265 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:85259454-85259616 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11267 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85261597-85262172 Neighboring gene Gse1 coiled-coil protein Neighboring gene ReSE screen-validated silencer GRCh37_chr16:85267436-85267602 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85267685-85268542 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7802 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7803 Neighboring gene microRNA 12128 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85272407-85272982 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:85274317-85275021 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85292052-85292756 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85292757-85293460 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85293461-85294165 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85300159-85300706 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85303550-85304252 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85305185-85306181 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85308847-85309819 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:85309820-85310793 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:85310794-85311766 Neighboring gene long intergenic non-protein coding RNA 311 Neighboring gene cytochrome c oxidase subunit 6C pseudogene 16

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_194037.1 

    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
    85227179..85227288
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    91293339..91293448
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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