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LOC114022701 Sharpr-MPRA regulatory region 11314 [ Homo sapiens (human) ]

Gene ID: 114022701, updated on 10-Oct-2023

Summary

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Gene symbol
LOC114022701
Gene description
Sharpr-MPRA regulatory region 11314
Gene type
biological region
Feature type(s)
regulatory: 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. It was validated as a functional repressive element by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Repressive DNase matched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Jan 2019]
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Genomic context

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See LOC114022701 in Genome Data Viewer
Location:
9q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (134449643..134449937)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (146666257..146666551)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (137341489..137341783)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137186973-137187694 Neighboring gene long intergenic non-protein coding RNA 2247 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137210088-137210946 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137210947-137211805 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20478 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20479 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20480 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137219587-137220516 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137220517-137221446 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137225116-137225782 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137225783-137226449 Neighboring gene NFE2L2 motif-containing MPRA enhancer 298 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137237611-137238182 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137241753-137242539 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137242540-137243325 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137243326-137244112 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137244113-137244897 Neighboring gene RXRA intron CAGE-defined high expression enhancer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137269547-137270338 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137270339-137271130 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137271131-137271922 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29276 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20481 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137276487-137276988 Neighboring gene retinoid X receptor alpha Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29278 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29280 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29279 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29277 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29281 Neighboring gene Sharpr-MPRA regulatory region 14205 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29282 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29283 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137288759-137289667 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137292875-137293376 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137293377-137293876 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137299715-137300527 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137298902-137299714 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137300528-137301339 Neighboring gene microRNA 4669 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137312909-137313409 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137325655-137326156 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137326157-137326656 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137328808-137329376 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137335184-137335762 Neighboring gene uncharacterized LOC105376311 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:137338907-137339314 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137346195-137347030 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137347374-137348311 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137348312-137349248 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137353764-137354264 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:137367387-137367888 Neighboring gene uncharacterized LOC100506532 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137385020-137385642 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137410305-137410805 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137414037-137414741 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137430547-137431179 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137437101-137437866 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137444755-137445276 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137445277-137445797 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137446661-137447263 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29285 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137481596-137482127 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137486667-137487168 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137494155-137495067 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137495068-137495979 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137518819-137519400 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137519401-137519982 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137534628-137535334 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137536590-137537174 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:137539157-137539956 Neighboring gene uncharacterized LOC124902300 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:137540681-137541180 Neighboring gene COL5A1 antisense RNA 1 Neighboring gene collagen type V alpha 1 chain

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_063918.1 

    Range
    101..395
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    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    134449643..134449937
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    146666257..146666551
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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