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Gene: LOC130057352 (ATAC-STARR-seq lymphoblastoid silent region 6574) Homo sapiens

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Symbol:

LOC130057352

Name:

ATAC-STARR-seq lymphoblastoid silent region 6574

RGD ID:

329820053

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 Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	15	67,066,039 - 67,066,198 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	15	67,358,377 - 67,358,536 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
T2T-CHM13v2.0	15	64,887,934 - 64,888,093 (+)	NCBI		T2T-CHM13v2.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
LOC130057352	Human	aortic aneurysm		IAGP	(Homo sapiens)	8554872	ClinVar Annotator: match by term: Aortic aneurysm	ClinVar	PMID:25741868
LOC130057352	Human	aortic valve disease 2		IAGP	(Homo sapiens)	8554872	ClinVar Annotator: match by term: Aortic valve disease 2	ClinVar	PMID:28492532
LOC130057352	Human	Ehlers-Danlos syndrome		IAGP	(Homo sapiens)	8554872	ClinVar Annotator: match by term: Ehlers-Danlos syndrome	ClinVar	PMID:25741868
LOC130057352	Human	Loeys-Dietz syndrome		IAGP	(Homo sapiens) and (Homo sapiens)	8554872	ClinVar Annotator: match by term: Loeys-Dietz syndrome	ClinVar
LOC130057352	Human	Loeys-Dietz syndrome		IAGP	(Homo sapiens)	8554872	ClinVar Annotator: match by term: Loeys-Dietz syndrome	ClinVar	PMID:25741868
LOC130057352	Human	Loeys-Dietz syndrome 3		IAGP	(Homo sapiens)	8554872	ClinVar Annotator: match by term: Loeys-Dietz syndrome 3	ClinVar	PMID:20851114 more ...
LOC130057352	Human	Loeys-Dietz syndrome 3		IAGP	(Homo sapiens) more ...	8554872	ClinVar more ...	ClinVar	PMID:25741868
LOC130057352	Human	Loeys-Dietz syndrome 3		IAGP	(Homo sapiens) more ...	8554872	ClinVar more ...	ClinVar	PMID:25741868 and PMID:28492532
LOC130057352	Human	Loeys-Dietz syndrome 3		IAGP	(Homo sapiens) more ...	8554872	ClinVar more ...	ClinVar
LOC130057352	Human	Loeys-Dietz syndrome 3		IAGP	(Homo sapiens)	8554872	ClinVar Annotator: match by term: Loeys-Dietz syndrome 3	ClinVar	PMID:24033266 and PMID:25741868
LOC130057352	Human	Loeys-Dietz syndrome 3		IAGP	(Homo sapiens)	8554872	ClinVar Annotator: match by term: Loeys-Dietz syndrome 3	ClinVar	PMID:25741868 more ...
LOC130057352	Human	Loeys-Dietz syndrome 3		IAGP	(Homo sapiens)	8554872	ClinVar Annotator: match by term: Loeys-Dietz syndrome and type 1C	ClinVar	PMID:25741868 and PMID:26333736
LOC130057352	Human	Loeys-Dietz syndrome 3		IAGP	(Homo sapiens)	8554872	ClinVar Annotator: match by term: Loeys-Dietz syndrome 3	ClinVar	PMID:28492532
LOC130057352	Human	thoracic aortic aneurysm		IAGP	(Homo sapiens) more ...	8554872	ClinVar Annotator: match by term: Thoracic aortic aneurysms and dissections	ClinVar	PMID:28492532
LOC130057352	Human	thoracic aortic aneurysm		IAGP	(Homo sapiens)	8554872	ClinVar Annotator: match by term: Thoracic aortic aneurysms and dissections	ClinVar	PMID:20851114 more ...
LOC130057352	Human	thoracic aortic aneurysm		IAGP	(Homo sapiens) more ...	8554872	ClinVar Annotator: match by term: Thoracic aortic aneurysms and dissections	ClinVar	PMID:25741868 and PMID:28492532
LOC130057352	Human	thoracic aortic aneurysm		IAGP	(Homo sapiens)	8554872	ClinVar Annotator: match by term: Thoracic aortic aneurysms and dissections	ClinVar	PMID:25741868 more ...
LOC130057352	Human	thoracic aortic aneurysm		IAGP	(Homo sapiens)	8554872	ClinVar Annotator: match by term: Thoracic aortic aneurysms and dissections	ClinVar	PMID:25741868 and PMID:30739908
LOC130057352	Human	thoracic aortic aneurysm		IAGP	(Homo sapiens)	8554872	ClinVar Annotator: match by term: Thoracic aortic aneurysms and dissections	ClinVar	PMID:24033266 and PMID:25741868
LOC130057352	Human	thoracic aortic aneurysm		IAGP	(Homo sapiens)	8554872	ClinVar Annotator: match by term: Thoracic aortic aneurysms and dissections	ClinVar	PMID:21778426 more ...
LOC130057352	Human	thoracic aortic aneurysm		IAGP	(Homo sapiens)	8554872	ClinVar Annotator: match by term: Thoracic aortic aneurysms and dissections	ClinVar	PMID:24711937 more ...
LOC130057352	Human	thoracic aortic aneurysm		IAGP	(Homo sapiens) more ...	8554872	ClinVar Annotator: match by term: Thoracic aortic aneurysms and dissections	ClinVar	PMID:25741868
LOC130057352	Human	thoracic aortic aneurysm		IAGP	(Homo sapiens) more ...	8554872	ClinVar Annotator: match by term: Thoracic aortic aneurysms and dissections	ClinVar	PMID:25741868 and PMID:28492532
LOC130057352	Human	thoracic aortic aneurysm		IAGP	(Homo sapiens) more ...	8554872	ClinVar more ...	ClinVar

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
LOC130057352	Human	Aortic aneurysm		IAGP	(Homo sapiens)	8554872	ClinVar Annotator: match by term: Aortic aneurysm	ClinVar	PMID:25741868

PMID:35858748

Variants in LOC130057352
43 total Variants

Name	Type	Condition(s)	Position(s)	Clinical significance
NM_005902.4(SMAD3):c.-11C>G	single nucleotide variant	Aneurysm-osteoarthritis syndrome [RCV004802685]	Chr15:67066144 [GRCh38] Chr15:67358482 [GRCh37] Chr15:15q22.33	uncertain significance
NM_005902.4(SMAD3):c.12C>T (p.Ile4=)	single nucleotide variant	Aneurysm-osteoarthritis syndrome [RCV001117315]\|Familial thoracic aortic aneurysm and aortic dissection [RCV001416536]	Chr15:67066166 [GRCh38] Chr15:67358504 [GRCh37] Chr15:15q22.33	likely benign\|uncertain significance
NM_005902.4(SMAD3):c.6G>A (p.Ser2=)	single nucleotide variant	Aneurysm-osteoarthritis syndrome [RCV004803326]\|Familial thoracic aortic aneurysm and aortic dissection [RCV001189204]	Chr15:67066160 [GRCh38] Chr15:67358498 [GRCh37] Chr15:15q22.33	likely benign
NM_005902.4(SMAD3):c.-28C>T	single nucleotide variant	Aneurysm-osteoarthritis syndrome [RCV000359576]\|Loeys-Dietz syndrome [RCV000318849]\|not specified [RCV000128166]	Chr15:67066127 [GRCh38] Chr15:67358465 [GRCh37] Chr15:15q22.33	benign
NM_005902.4(SMAD3):c.21del (p.Phe7fs)	deletion	Familial thoracic aortic aneurysm and aortic dissection [RCV001179189]	Chr15:67066175 [GRCh38] Chr15:67358513 [GRCh37] Chr15:15q22.33	pathogenic
NM_005902.4(SMAD3):c.-15G>A	single nucleotide variant	Aneurysm-osteoarthritis syndrome [RCV000378447]\|Familial thoracic aortic aneurysm and aortic dissection [RCV000288615]\|not provided [RCV004714504]\|not specified [RCV000128168]	Chr15:67066140 [GRCh38] Chr15:67358478 [GRCh37] Chr15:15q22.33	benign
NM_005902.4(SMAD3):c.23C>G (p.Thr8Ser)	single nucleotide variant	Familial thoracic aortic aneurysm and aortic dissection [RCV001948166]	Chr15:67066177 [GRCh38] Chr15:67358515 [GRCh37] Chr15:15q22.33	uncertain significance
NM_005902.4(SMAD3):c.30G>T (p.Pro10=)	single nucleotide variant	Aneurysm-osteoarthritis syndrome [RCV003641011]\|Familial thoracic aortic aneurysm and aortic dissection [RCV002325970]	Chr15:67066184 [GRCh38] Chr15:67358522 [GRCh37] Chr15:15q22.33	likely benign\|conflicting interpretations of pathogenicity
NM_005902.4(SMAD3):c.-1C>T	single nucleotide variant	Familial thoracic aortic aneurysm and aortic dissection [RCV001184772]\|not provided [RCV000329392]	Chr15:67066154 [GRCh38] Chr15:67358492 [GRCh37] Chr15:15q22.33	uncertain significance
NM_005902.4(SMAD3):c.-38C>T	single nucleotide variant	Aneurysm-osteoarthritis syndrome [RCV001115860]	Chr15:67066117 [GRCh38] Chr15:67358455 [GRCh37] Chr15:15q22.33	uncertain significance
NM_005902.4(SMAD3):c.3G>A (p.Met1Ile)	single nucleotide variant	Aneurysm-osteoarthritis syndrome [RCV001799526]\|Familial thoracic aortic aneurysm and aortic dissection [RCV002377898]	Chr15:67066157 [GRCh38] Chr15:67358495 [GRCh37] Chr15:15q22.33	pathogenic\|likely pathogenic
NM_005902.4(SMAD3):c.5C>A (p.Ser2Ter)	single nucleotide variant	Familial thoracic aortic aneurysm and aortic dissection [RCV001218505]\|not provided [RCV000521242]	Chr15:67066159 [GRCh38] Chr15:67358497 [GRCh37] Chr15:15q22.33	pathogenic\|likely pathogenic
NM_005902.4(SMAD3):c.36G>A (p.Val12=)	single nucleotide variant	Familial thoracic aortic aneurysm and aortic dissection [RCV000774105]	Chr15:67066190 [GRCh38] Chr15:67358528 [GRCh37] Chr15:15q22.33	likely benign
NM_005902.4(SMAD3):c.-10C>T	single nucleotide variant	Ehlers-Danlos syndrome [RCV002276654]\|Familial thoracic aortic aneurysm and aortic dissection [RCV001182314]	Chr15:67066145 [GRCh38] Chr15:67358483 [GRCh37] Chr15:15q22.33	uncertain significance
NM_005902.4(SMAD3):c.1A>T (p.Met1Leu)	single nucleotide variant	Aneurysm-osteoarthritis syndrome [RCV001195952]\|Familial thoracic aortic aneurysm and aortic dissection [RCV001231422]	Chr15:67066155 [GRCh38] Chr15:67358493 [GRCh37] Chr15:15q22.33	pathogenic\|likely pathogenic
NM_005902.4(SMAD3):c.-23C>T	single nucleotide variant	Aneurysm-osteoarthritis syndrome [RCV000323863]\|Loeys-Dietz syndrome [RCV000264993]\|not provided [RCV004715738]\|not specified [RCV000128167]	Chr15:67066132 [GRCh38] Chr15:67358470 [GRCh37] Chr15:15q22.33	benign
NM_005902.4(SMAD3):c.15G>A (p.Leu5=)	single nucleotide variant	Familial thoracic aortic aneurysm and aortic dissection [RCV002880921]	Chr15:67066169 [GRCh38] Chr15:67358507 [GRCh37] Chr15:15q22.33	likely benign
GRCh38/hg38 15q22.2-26.3(chr15:59828460-101920998)x3	copy number gain	See cases [RCV000142915]	Chr15:59828460..101920998 [GRCh38] Chr15:60120659..102461201 [GRCh37] Chr15:57907951..100278724 [NCBI36] Chr15:15q22.2-26.3	pathogenic
NC_000015.10:g.(?_66703239)_(67066380_?)del	deletion	Aortic valve disease 2 [RCV003117503]\|Familial thoracic aortic aneurysm and aortic dissection [RCV000708534]	Chr15:66703239..67066380 [GRCh38] Chr15:66995577..67358718 [GRCh37] Chr15:15q22.31-22.33	pathogenic\|uncertain significance
NM_005902.4(SMAD3):c.-2C>G	single nucleotide variant	Familial thoracic aortic aneurysm and aortic dissection [RCV001185436]	Chr15:67066153 [GRCh38] Chr15:67358491 [GRCh37] Chr15:15q22.33	uncertain significance
NM_005902.4(SMAD3):c.36G>C (p.Val12=)	single nucleotide variant	Familial thoracic aortic aneurysm and aortic dissection [RCV003060326]	Chr15:67066190 [GRCh38] Chr15:67358528 [GRCh37] Chr15:15q22.33	likely benign
NM_005902.4(SMAD3):c.1A>C (p.Met1Leu)	single nucleotide variant	Familial thoracic aortic aneurysm and aortic dissection [RCV002315227]	Chr15:67066155 [GRCh38] Chr15:67358493 [GRCh37] Chr15:15q22.33	pathogenic\|likely pathogenic
NC_000015.10:g.(?_66703239)_(67190556_?)del	deletion	Familial thoracic aortic aneurysm and aortic dissection [RCV000813979]	Chr15:66703239..67190556 [GRCh38] Chr15:66995577..67482894 [GRCh37] Chr15:15q22.31-22.33	pathogenic
NM_005902.4(SMAD3):c.30G>A (p.Pro10=)	single nucleotide variant	not provided [RCV002292900]	Chr15:67066184 [GRCh38] Chr15:67358522 [GRCh37] Chr15:15q22.33	likely benign
NM_005902.4(SMAD3):c.27C>T (p.Pro9=)	single nucleotide variant	Aneurysm-osteoarthritis syndrome [RCV004004129]\|Familial thoracic aortic aneurysm and aortic dissection [RCV000654832]\|SMAD3-related disorder [RCV004533429]	Chr15:67066181 [GRCh38] Chr15:67358519 [GRCh37] Chr15:15q22.33	benign\|likely benign
NM_005902.4(SMAD3):c.-115C>T	single nucleotide variant	Familial thoracic aortic aneurysm and aortic dissection [RCV000276717]\|Loeys-Dietz syndrome [RCV000299183]	Chr15:67066040 [GRCh38] Chr15:67358378 [GRCh37] Chr15:15q22.33	likely benign
NM_005902.4(SMAD3):c.28C>G (p.Pro10Ala)	single nucleotide variant	Aneurysm-osteoarthritis syndrome [RCV004703279]	Chr15:67066182 [GRCh38] Chr15:67358520 [GRCh37] Chr15:15q22.33	likely pathogenic\|uncertain significance
NM_005902.4(SMAD3):c.29dup (p.Ile11fs)	duplication	Familial thoracic aortic aneurysm and aortic dissection [RCV002435607]	Chr15:67066178..67066179 [GRCh38] Chr15:67358516..67358517 [GRCh37] Chr15:15q22.33	pathogenic
NM_005902.4(SMAD3):c.-18C>T	single nucleotide variant	not specified [RCV000608741]	Chr15:67066137 [GRCh38] Chr15:67358475 [GRCh37] Chr15:15q22.33	likely benign
NM_005902.4(SMAD3):c.1A>G (p.Met1Val)	single nucleotide variant	Aortic aneurysm [RCV001526579]	Chr15:67066155 [GRCh38] Chr15:67358493 [GRCh37] Chr15:15q22.33	pathogenic
NM_005902.4(SMAD3):c.17C>T (p.Pro6Leu)	single nucleotide variant	not provided [RCV000197181]	Chr15:67066171 [GRCh38] Chr15:67358509 [GRCh37] Chr15:15q22.33	uncertain significance
NM_005902.4(SMAD3):c.34G>T (p.Val12Leu)	single nucleotide variant	Familial thoracic aortic aneurysm and aortic dissection [RCV000526860]	Chr15:67066188 [GRCh38] Chr15:67358526 [GRCh37] Chr15:15q22.33	uncertain significance
NM_005902.4(SMAD3):c.-100C>T	single nucleotide variant	Aneurysm-osteoarthritis syndrome [RCV000354002]\|Familial thoracic aortic aneurysm and aortic dissection [RCV000263645]	Chr15:67066055 [GRCh38] Chr15:67358393 [GRCh37] Chr15:15q22.33	uncertain significance
NM_005902.4(SMAD3):c.9C>T (p.Ser3=)	single nucleotide variant	Aneurysm-osteoarthritis syndrome [RCV003999038]\|Familial thoracic aortic aneurysm and aortic dissection [RCV002518697]	Chr15:67066163 [GRCh38] Chr15:67358501 [GRCh37] Chr15:15q22.33	likely benign
NM_005902.4(SMAD3):c.5C>G (p.Ser2Trp)	single nucleotide variant	Familial thoracic aortic aneurysm and aortic dissection [RCV003172510]\|not provided [RCV004801327]	Chr15:67066159 [GRCh38] Chr15:67358497 [GRCh37] Chr15:15q22.33	uncertain significance
NM_005902.4(SMAD3):c.-17_-15delinsACA	indel	Familial thoracic aortic aneurysm and aortic dissection [RCV001526317]	Chr15:67066138..67066140 [GRCh38] Chr15:67358476..67358478 [GRCh37] Chr15:15q22.33	uncertain significance
NM_005902.4(SMAD3):c.33C>T (p.Ile11=)	single nucleotide variant	Aneurysm-osteoarthritis syndrome [RCV004005924]\|Familial thoracic aortic aneurysm and aortic dissection [RCV003643481]	Chr15:67066187 [GRCh38] Chr15:67358525 [GRCh37] Chr15:15q22.33	likely benign
NM_005902.4(SMAD3):c.41G>C (p.Arg14Pro)	single nucleotide variant	Familial thoracic aortic aneurysm and aortic dissection [RCV003876482]	Chr15:67066195 [GRCh38] Chr15:67358533 [GRCh37] Chr15:15q22.33	uncertain significance
NM_005902.4(SMAD3):c.25C>T (p.Pro9Ser)	single nucleotide variant	Aneurysm-osteoarthritis syndrome [RCV004005887]\|Familial thoracic aortic aneurysm and aortic dissection [RCV003642766]	Chr15:67066179 [GRCh38] Chr15:67358517 [GRCh37] Chr15:15q22.33	uncertain significance
NM_005902.4(SMAD3):c.11T>C (p.Ile4Thr)	single nucleotide variant	Familial thoracic aortic aneurysm and aortic dissection [RCV004523813]	Chr15:67066165 [GRCh38] Chr15:67358503 [GRCh37] Chr15:15q22.33	uncertain significance
NM_005902.4(SMAD3):c.-5C>T	single nucleotide variant	Aneurysm-osteoarthritis syndrome [RCV004015641]	Chr15:67066150 [GRCh38] Chr15:67358488 [GRCh37] Chr15:15q22.33	uncertain significance
NM_005902.4(SMAD3):c.2T>C (p.Met1Thr)	single nucleotide variant	Aneurysm-osteoarthritis syndrome [RCV004016898]	Chr15:67066156 [GRCh38] Chr15:67358494 [GRCh37] Chr15:15q22.33	likely pathogenic
NM_005902.4(SMAD3):c.24T>C (p.Thr8=)	single nucleotide variant	Familial thoracic aortic aneurysm and aortic dissection [RCV004821769]	Chr15:67066178 [GRCh38] Chr15:67358516 [GRCh37] Chr15:15q22.33	likely benign
NM_005902.4(SMAD3):c.13C>T (p.Leu5=)	single nucleotide variant	Aneurysm-osteoarthritis syndrome [RCV004013257]	Chr15:67066167 [GRCh38] Chr15:67358505 [GRCh37] Chr15:15q22.33	likely benign
NM_005902.4(SMAD3):c.-5C>A	single nucleotide variant	Aneurysm-osteoarthritis syndrome [RCV004013311]	Chr15:67066150 [GRCh38] Chr15:67358488 [GRCh37] Chr15:15q22.33	uncertain significance
NM_005902.4(SMAD3):c.-5del	deletion	Aneurysm-osteoarthritis syndrome [RCV004013719]	Chr15:67066147 [GRCh38] Chr15:67358485 [GRCh37] Chr15:15q22.33	uncertain significance
NM_005902.4(SMAD3):c.24T>G (p.Thr8=)	single nucleotide variant	Aneurysm-osteoarthritis syndrome [RCV004014248]\|Familial thoracic aortic aneurysm and aortic dissection [RCV005103343]	Chr15:67066178 [GRCh38] Chr15:67358516 [GRCh37] Chr15:15q22.33	likely benign

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.


RefSeq Transcripts	NG_191773	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC087482	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CP068263	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Database	Acc Id	Source(s)
COSMIC	LOC130057352	COSMIC
GTEx	LOC130057352	GTEx
Human Proteome Map	LOC130057352	Human Proteome Map
NCBI Gene	LOC130057352	ENTREZGENE

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailable


InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailable


Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
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