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LOC121466715 Sharpr-MPRA regulatory region 3381 [ Homo sapiens (human) ]

Gene ID: 121466715, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121466715
Gene description
Sharpr-MPRA regulatory region 3381
Gene type
biological region
Feature type(s)
regulatory: enhancer, transcriptional_cis_regulatory_region
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 an enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 9:DNaseU, primarily UW DNase, weaker open chromatin sites). Four overlapping subregions containing Neanderthal adaptively introgressed genetic variants were also validated as enhancers by MPRAs in K562 erythroleukemia cells, with activity observed for both the introgressed and non-introgressed variant alleles, and with one variant, 12:113364375 or rs61478890, being an expression-modulating variant (emVar). [provided by RefSeq, Sep 2023]
Annotation information
Note: This locus has been reviewed for its involvement in coronavirus biology, and is regulatory element in the vicinity of coronavirus related gene(s).
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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 (112926442..112926798)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (112903129..112903486)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (113364309..113364603)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene protein tyrosine phosphatase non-receptor type 11 Neighboring gene uncharacterized LOC124903024 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:112954684-112955184 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:113015949-113016468 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:113018366-113018890 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:113039985-113040713 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:113055106-113055606 Neighboring gene rabphilin 3A Neighboring gene NANOG hESC enhancer GRCh37_chr12:113079622-113080142 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:113147969-113148469 Neighboring gene microRNA 1302-1 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr12:113185662-113186162 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:113229645-113230186 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:113306366-113306564 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7051 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7052 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24142 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_24146 and experimental_24152 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24159 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24163 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_24171 and experimental_24176 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_24215 and experimental_24231 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_24264 and experimental_24270 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_24293 and experimental_24295 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_24298, experimental_24301 and experimental_24306 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_24317/24320 and experimental_24338 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_24357 and experimental_24368 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24404 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24448 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_24456 and experimental_24461 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24463 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24487 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7053 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24505 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4887 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24515 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24520 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24535 Neighboring gene MPRA-validated peak1965 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:113400746-113401246 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:113401247-113401747 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24547 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24553 Neighboring gene 2'-5'-oligoadenylate synthetase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7054 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7055 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7056 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7057 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24560 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24566 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24567 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:113444541-113445740 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24568 Neighboring gene 2'-5'-oligoadenylate synthetase 3 Neighboring gene 2'-5'-oligoadenylate synthetase 2

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)

General gene information

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Other Names

  • Neanderthal introgressed variant-containing enhancer experimental_24275
  • Neanderthal introgressed variant-containing enhancer experimental_24278
  • Neanderthal introgressed variant-containing enhancer experimental_24281
  • Neanderthal introgressed variant-containing enhancer experimental_24287
  • emVar-containing allelic enhancer experimental_24278

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_074648.2 

    Range
    101..457
    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
    112926442..112926798
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    112903129..112903486
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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