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LOC130003167 ATAC-STARR-seq lymphoblastoid active region 2901 [ Homo sapiens (human) ]

Gene ID: 130003167, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130003167
Gene description
ATAC-STARR-seq lymphoblastoid active region 2901
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 LOC130003167 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 (1359445..1359524)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (1358346..1358425)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (1401640..1401719)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:1201744-1202634 Neighboring gene uncharacterized LOC105376344 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:1219106-1219608 Neighboring gene long intergenic non-protein coding RNA 200 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:1230396-1230996 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:1234984-1236183 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:1237029-1237528 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:1256314-1256814 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:1258172-1258702 Neighboring gene adenosine deaminase RNA specific B2 (inactive) Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:1283673-1284184 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:1284185-1284695 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:1297166-1297666 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:1297667-1298167 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:1312697-1313582 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:1315089-1315589 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:1313583-1314467 Neighboring gene MPRA-validated peak840 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:1334566-1335464 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:1335779-1336688 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:1351707-1352350 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:1352351-1352995 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:1352996-1353639 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:1354285-1354928 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:1354929-1355573 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:1386449-1387132 Neighboring gene uncharacterized LOC105376342 Neighboring gene Sharpr-MPRA regulatory region 10920 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:1421674-1422378 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:1422379-1423081 Neighboring gene NANOG hESC enhancer GRCh37_chr10:1423311-1423822 Neighboring gene uncharacterized LOC124902364 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:1449419-1450003 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr10:1451683-1452882

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_182613.1 

    Range
    101..180
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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
    1359445..1359524
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    1358346..1358425
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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