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LOC130008636 ATAC-STARR-seq lymphoblastoid active region 6937 [ Homo sapiens (human) ]

Gene ID: 130008636, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130008636
Gene description
ATAC-STARR-seq lymphoblastoid active region 6937
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 LOC130008636 in Genome Data Viewer
Location:
chromosome: 12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (104865328..104865457)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (104826945..104827074)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (105259106..105259235)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene carbohydrate sulfotransferase 11 Neighboring gene ATP synthase F(0) complex subunit C1, mitochondrial-like Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6921 Neighboring gene Sharpr-MPRA regulatory region 14866 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:104920569-104921159 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6922 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:104949096-104949598 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:104950760-104951594 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23947 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6923 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6924 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6925 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6926 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6927 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:104997281-104997908 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:104997909-104998535 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:104998957-104999544 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:104999545-105000132 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr12:105017531-105018268 Neighboring gene microRNA 3922 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:105026139-105026640 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6928 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6929 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:105065189-105065793 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:105081721-105081916 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6930 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6931 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:105102028-105102832 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:105102833-105103637 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6932 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:105114284-105114912 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:105116877-105117495 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6934 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:105136527-105137148 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:105144840-105145417 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6935 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6936 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24027 Neighboring gene Sharpr-MPRA regulatory region 12146 Neighboring gene solute carrier family 41 member 2 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24038 Neighboring gene Sharpr-MPRA regulatory region 3023 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6938 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4799 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4800 Neighboring gene uncharacterized LOC105369952 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:105379748-105380260 Neighboring gene keratin 18 pseudogene 20 Neighboring gene NOP protein chaperone 1

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_187205.1 

    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    104865328..104865457
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    104826945..104827074
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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