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LOC130057963 ATAC-STARR-seq lymphoblastoid active region 10112 [ Homo sapiens (human) ]

Gene ID: 130057963, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130057963
Gene description
ATAC-STARR-seq lymphoblastoid active region 10112
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 LOC130057963 in Genome Data Viewer
Location:
chromosome: 15
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (92622206..92622345)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (90384647..90384786)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (93165436..93165575)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene chromosome 15 putative open reading frame 32 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:93053451-93053972 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:93061329-93061830 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:93064789-93065381 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:93105459-93105998 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:93105999-93106536 Neighboring gene long intergenic non-protein coding RNA 930 Neighboring gene MPRA-validated peak2428 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:93156777-93157278 Neighboring gene uncharacterized LOC124903559 Neighboring gene family with sequence similarity 174 member B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10113 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10114 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:93186854-93187634 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:93187635-93188414 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:93190755-93191534 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6840 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6841 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6842 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6843 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10116 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10117 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:93207617-93208116 Neighboring gene Sharpr-MPRA regulatory region 7580 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_42675 Neighboring gene high mobility group nucleosome binding domain 1 pseudogene 38

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_192384.1 

    Range
    101..240
    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    92622206..92622345
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    90384647..90384786
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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