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LOC112163602 Sharpr-MPRA regulatory region 9853 [ Homo sapiens (human) ]

Gene ID: 112163602, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112163602
Gene description
Sharpr-MPRA regulatory region 9853
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
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 was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. A subregion was validated as a functional enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 1:Tss). This locus also includes two accessible chromatin subregions, one of which was validated as an enhancer and the other as a silencer based on their ability to activate or repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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Location:
12q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (51238605..51239072)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (51201501..51201968)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (51632389..51632683)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902933 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4459 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6372 Neighboring gene POU class 6 homeobox 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:51593597-51594096 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4460 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4461 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4462 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6373 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:51614127-51614306 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:51631660-51632297 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:51633573-51634209 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:51641233-51641734 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:51641735-51642234 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:51642235-51642736 Neighboring gene DAZ associated protein 2 Neighboring gene small cell adhesion glycoprotein Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:51663873-51664373 Neighboring gene bridging integrator 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6375 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6376 Neighboring gene Sharpr-MPRA regulatory region 8177 Neighboring gene uncharacterized LOC105369767 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6377 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4466

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. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, Free PMC Article
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. 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)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 6374
  • ATAC-STARR-seq lymphoblastoid silent region 4463

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_056584.2 

    Range
    101..568
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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
    51238605..51239072
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    51201501..51201968
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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