LOC129937389 (ATAC-STARR-seq lymphoblastoid silent region 14645) - Rat Genome Database

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Gene: LOC129937389 (ATAC-STARR-seq lymphoblastoid silent region 14645) Homo sapiens
Analyze
Symbol: LOC129937389
Name: ATAC-STARR-seq lymphoblastoid silent region 14645
RGD ID: 329403257
Description: This genomic sequence represents an accessible chromatin region that was validated as a silencer based on its ability to 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) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
Type: biological-region
RefSeq Status: REVIEWED
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383122,794,906 - 122,795,395 (+)NCBIGRCh38GRCh38hg38GRCh38
T2T-CHM13v2.03125,514,095 - 125,514,584 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
ovarian cancer  (IAGP)

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References
Additional References at PubMed
PMID:35858748  


Genomics

Variants

.
Variants in LOC129937389
4 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 3q11.1-21.2(chr3:93979547-124774010)x1 copy number loss Chromosome 3q13.31 deletion syndrome [RCV003327614] Chr3:93979547..124774010 [GRCh38]
Chr3:3q11.1-21.2		 pathogenic
Single allele duplication not specified [RCV002286365] Chr3:122157406..123113479 [GRCh38]
Chr3:3q13.33-21.1		 uncertain significance
GRCh38/hg38 3q13.33-21.2(chr3:121644209-125676353)x1 copy number loss See cases [RCV000051569] Chr3:121644209..125676353 [GRCh38]
Chr3:121363056..125395197 [GRCh37]
Chr3:122845746..126877887 [NCBI36]
Chr3:3q13.33-21.2		 pathogenic
GRCh38/hg38 3q13.32-21.2(chr3:119117166-125920734)x1 copy number loss See cases [RCV000051546] Chr3:119117166..125920734 [GRCh38]
Chr3:118836013..125639577 [GRCh37]
Chr3:120318703..127122267 [NCBI36]
Chr3:3q13.32-21.2		 pathogenic
GRCh38/hg38 3q11.1-21.1(chr3:93886671-123216683)x1 copy number loss See cases [RCV000051543] Chr3:93886671..123216683 [GRCh38]
Chr3:93605515..122935530 [GRCh37]
Chr3:95088205..124418220 [NCBI36]
Chr3:3q11.1-21.1		 pathogenic
GRCh38/hg38 3q11.1-24(chr3:93800620-145695381)x3 copy number gain See cases [RCV000142340] Chr3:93800620..145695381 [GRCh38]
Chr3:93519464..145413168 [GRCh37]
Chr3:95002154..146895858 [NCBI36]
Chr3:3q11.1-24		 pathogenic
GRCh38/hg38 3q13.11-29(chr3:103426882-198110178)x3 copy number gain See cases [RCV000134948] Chr3:103426882..198110178 [GRCh38]
Chr3:103145726..197837049 [GRCh37]
Chr3:104628416..199321446 [NCBI36]
Chr3:3q13.11-29		 pathogenic
GRCh38/hg38 3q13.33-21.3(chr3:121925147-126782249)x1 copy number loss See cases [RCV000140814] Chr3:121925147..126782249 [GRCh38]
Chr3:121643994..126501092 [GRCh37]
Chr3:123126684..127983782 [NCBI36]
Chr3:3q13.33-21.3		 pathogenic
GRCh38/hg38 3q13.32-21.3(chr3:118673898-126540730)x1 copy number loss See cases [RCV000143695] Chr3:118673898..126540730 [GRCh38]
Chr3:118392745..126259573 [GRCh37]
Chr3:119875435..127742263 [NCBI36]
Chr3:3q13.32-21.3		 pathogenic
GRCh38/hg38 3q13.2-21.3(chr3:112620977-128734134)x1 copy number loss See cases [RCV000139033] Chr3:112620977..128734134 [GRCh38]
Chr3:112339824..128452977 [GRCh37]
Chr3:113822514..129935667 [NCBI36]
Chr3:3q13.2-21.3		 pathogenic
GRCh38/hg38 3q13.31-21.2(chr3:114122562-124532374)x1 copy number loss See cases [RCV000142009] Chr3:114122562..124532374 [GRCh38]
Chr3:113841409..124251221 [GRCh37]
Chr3:115324099..125733911 [NCBI36]
Chr3:3q13.31-21.2		 pathogenic
NM_032839.3(SLC49A4):c.112C>T (p.Pro38Ser) single nucleotide variant Ovarian cancer [RCV003154687] Chr3:122795304 [GRCh38]
Chr3:122514151 [GRCh37]
Chr3:3q21.1		 benign
NM_032839.3(SLC49A4):c.58G>C (p.Gly20Arg) single nucleotide variant not specified [RCV004337911] Chr3:122795250 [GRCh38]
Chr3:122514097 [GRCh37]
Chr3:3q21.1		 uncertain significance
NM_032839.3(SLC49A4):c.94G>A (p.Ala32Thr) single nucleotide variant not specified [RCV004312939] Chr3:122795286 [GRCh38]
Chr3:122514133 [GRCh37]
Chr3:3q21.1		 uncertain significance
NM_032839.3(SLC49A4):c.107C>T (p.Ala36Val) single nucleotide variant not specified [RCV004274657] Chr3:122795299 [GRCh38]
Chr3:122514146 [GRCh37]
Chr3:3q21.1		 uncertain significance
NM_032839.3(SLC49A4):c.62C>G (p.Pro21Arg) single nucleotide variant not specified [RCV004461879] Chr3:122795254 [GRCh38]
Chr3:122514101 [GRCh37]
Chr3:3q21.1		 uncertain significance
NM_032839.3(SLC49A4):c.133G>T (p.Gly45Trp) single nucleotide variant not specified [RCV004461874] Chr3:122795325 [GRCh38]
Chr3:122514172 [GRCh37]
Chr3:3q21.1		 uncertain significance
NM_032839.3(SLC49A4):c.76T>A (p.Ser26Thr) single nucleotide variant not specified [RCV004461881] Chr3:122795268 [GRCh38]
Chr3:122514115 [GRCh37]
Chr3:3q21.1		 uncertain significance

Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC129937389 COSMIC
GTEx LOC129937389 GTEx
Human Proteome Map LOC129937389 Human Proteome Map
NCBI Gene LOC129937389 ENTREZGENE