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LOC130003160 ATAC-STARR-seq lymphoblastoid active region 2893 [ Homo sapiens (human) ]

Gene ID: 130003160, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130003160
Gene description
ATAC-STARR-seq lymphoblastoid active region 2893
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 LOC130003160 in Genome Data Viewer
Location:
chromosome: 10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (1036094..1036143)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (1033236..1033285)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (1082034..1082083)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene La ribonucleoprotein 4B Neighboring gene keratinocyte proline-rich protein-like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:989167-989668 Neighboring gene LARP4B divergent transcript Neighboring gene Sharpr-MPRA regulatory region 2332 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:1036121-1037016 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:1050745-1051244 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:1054558-1055058 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:1055059-1055559 Neighboring gene GTP binding protein 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2894 Neighboring gene IDI2 antisense RNA 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:1088961-1090160 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr10:1094306-1094836 and GRCh37_chr10:1094837-1095366 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:1095367-1095896 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2066 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2897 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2067 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2898 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2899 Neighboring gene isopentenyl-diphosphate delta isomerase 2 Neighboring gene isopentenyl-diphosphate delta isomerase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:1130525-1131024 Neighboring gene WD repeat domain 37 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr10:1141578-1142777 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:1148139-1148671 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr10:1155609-1156808 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:1163429-1163930 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:1166460-1167101 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:1167102-1167742 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:1196487-1196986 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:1199503-1200004 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:1200005-1200504 Neighboring gene uncharacterized LOC105376344 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:1201744-1202634

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_182606.1 

    Range
    101..150
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    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    1036094..1036143
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    1033236..1033285
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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