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LOC112935950 Sharpr-MPRA regulatory region 8375 [ Homo sapiens (human) ]

Gene ID: 112935950, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112935950
Gene description
Sharpr-MPRA regulatory region 8375
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 was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as a functional enhancer by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 18:Pol2, Pol2 specific locations, majority in genes but substantial portion in intergenic locations), with weak activation in HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 18:Pol2). [provided by RefSeq, Aug 2018]
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Genomic context

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See LOC112935950 in Genome Data Viewer
Location:
3p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (53194173..53194467)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (53227052..53227346)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (53228189..53228483)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19950 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:53106949-53107566 Neighboring gene Sharpr-MPRA regulatory region 3047 Neighboring gene RFT1 homolog Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19952 Neighboring gene NANOG hESC enhancer GRCh37_chr3:53136831-53137332 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19953 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:53148350-53149549 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19954 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19957 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19956 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19955 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:53182771-53183578 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:53190496-53190996 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19958 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14459 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14460 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19959 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19960 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:53201730-53202410 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:53202411-53203091 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14461 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19961 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:53208863-53209718 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19962 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19963 Neighboring gene protein kinase C delta Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19964 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19966 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19967 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14462 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:53236717-53237216 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14463 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:53261945-53263144 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:53270389-53271197 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:53274891-53275886 Neighboring gene transketolase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14464 Neighboring gene Sharpr-MPRA regulatory region 10976 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:53303617-53304816 Neighboring gene uncharacterized LOC107986087 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:53305434-53306319 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:53307415-53307967 Neighboring gene small nucleolar RNA U13

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

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_061464.1 

    Range
    101..395
    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    53194173..53194467
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    53227052..53227346
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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