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LOC130004650 ATAC-STARR-seq lymphoblastoid active region 3973 [ Homo sapiens (human) ]

Gene ID: 130004650, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130004650
Gene description
ATAC-STARR-seq lymphoblastoid active region 3973
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 LOC130004650 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 (103763619..103763748)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (104650918..104651047)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (105523377..105523506)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene SH3 and PX domains 2A Neighboring gene uncharacterized LOC124902495 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3968 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3967 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105441739-105442519 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3969 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3970 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3971 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105451952-105452918 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105455468-105456214 Neighboring gene NFE2L2 motif-containing MPRA enhancer 292 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105467435-105468414 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105468415-105469393 Neighboring gene NANOG hESC enhancer GRCh37_chr10:105482339-105482840 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105491951-105492499 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105492500-105493047 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105505582-105506103 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105506520-105507020 Neighboring gene SH3PXD2A antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105507021-105507521 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105515685-105516342 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105516343-105516998 Neighboring gene Sharpr-MPRA regulatory region 10495 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3974 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2789 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105531100-105532070 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105539219-105539718 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105544793-105545294 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105549545-105550545 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:105560029-105560530 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2790 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105563531-105564374 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105567495-105567996 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105594413-105594969 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105594970-105595525 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105667461-105668062 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 10:105668179 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105677593-105678238 Neighboring gene STN1 subunit of CST complex Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:105686883-105687548 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105688215-105688880 Neighboring gene uncharacterized LOC102724351 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2792

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_184095.1 

    Range
    101..230
    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    103763619..103763748
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    104650918..104651047
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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