Name: rs7254521
Published: September 21, 2022
License: Open Access

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs7254521

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr19:11132746 (GRCh38.p14) Help
The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.
Alleles: C>A / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.127032 (33624/264690, TOPMED)
T=0.00634 (179/28230, 14KJPN)
T=0.00668 (112/16760, 8.3KJPN) (+ 13 more)
T=0.05870 (932/15876, ALFA)
T=0.1099 (704/6404, 1000G_30x)
T=0.1104 (553/5008, 1000G)
T=0.1293 (579/4478, Estonian)
T=0.1269 (489/3854, ALSPAC)
T=0.1467 (544/3708, TWINSUK)
T=0.0069 (20/2918, KOREAN)
T=0.152 (91/598, NorthernSweden)
T=0.125 (27/216, Qatari)
C=0.425 (51/120, SGDP_PRJ)
T=0.12 (11/90, PharmGKB)
T=0.10 (4/40, GENOME_DK)
C=0.4 (4/10, Siberian)

Clinical Significance: Reported in ClinVar
Gene : Consequence: LDLR : 3 Prime UTR Variant
Publications: 1 citation
Genomic View: See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	15876	C=0.94130	A=0.00000, T=0.05870	0.889645	0.007055	0.103301	18
European	Sub	12318	C=0.92888	A=0.00000, T=0.07112	0.866374	0.008605	0.12502	10
African	Sub	2178	C=0.9904	A=0.0000, T=0.0096	0.980716	0.0	0.019284	0
African Others	Sub	86	C=0.99	A=0.00, T=0.01	0.976744	0.0	0.023256	0
African American	Sub	2092	C=0.9904	A=0.0000, T=0.0096	0.98088	0.0	0.01912	0
Asian	Sub	112	C=1.000	A=0.000, T=0.000	1.0	0.0	0.0	N/A
East Asian	Sub	86	C=1.00	A=0.00, T=0.00	1.0	0.0	0.0	N/A
Other Asian	Sub	26	C=1.00	A=0.00, T=0.00	1.0	0.0	0.0	N/A
Latin American 1	Sub	104	C=1.000	A=0.000, T=0.000	1.0	0.0	0.0	N/A
Latin American 2	Sub	508	C=1.000	A=0.000, T=0.000	1.0	0.0	0.0	N/A
South Asian	Sub	68	C=1.00	A=0.00, T=0.00	1.0	0.0	0.0	N/A
Other	Sub	588	C=0.940	A=0.000, T=0.060	0.891156	0.010204	0.098639	3

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	C=0.872968	T=0.127032
14KJPN	JAPANESE	Study-wide	28230	C=0.99366	T=0.00634
8.3KJPN	JAPANESE	Study-wide	16760	C=0.99332	T=0.00668
Allele Frequency Aggregator	Total	Global	15876	C=0.94130	A=0.00000, T=0.05870
Allele Frequency Aggregator	European	Sub	12318	C=0.92888	A=0.00000, T=0.07112
Allele Frequency Aggregator	African	Sub	2178	C=0.9904	A=0.0000, T=0.0096
Allele Frequency Aggregator	Other	Sub	588	C=0.940	A=0.000, T=0.060
Allele Frequency Aggregator	Latin American 2	Sub	508	C=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	Asian	Sub	112	C=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	104	C=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	South Asian	Sub	68	C=1.00	A=0.00, T=0.00
1000Genomes_30x	Global	Study-wide	6404	C=0.8901	T=0.1099
1000Genomes_30x	African	Sub	1786	C=0.8522	T=0.1478
1000Genomes_30x	Europe	Sub	1266	C=0.8412	T=0.1588
1000Genomes_30x	South Asian	Sub	1202	C=0.8760	T=0.1240
1000Genomes_30x	East Asian	Sub	1170	C=0.9966	T=0.0034
1000Genomes_30x	American	Sub	980	C=0.912	T=0.088
1000Genomes	Global	Study-wide	5008	C=0.8896	T=0.1104
1000Genomes	African	Sub	1322	C=0.8449	T=0.1551
1000Genomes	East Asian	Sub	1008	C=0.9970	T=0.0030
1000Genomes	Europe	Sub	1006	C=0.8390	T=0.1610
1000Genomes	South Asian	Sub	978	C=0.870	T=0.130
1000Genomes	American	Sub	694	C=0.919	T=0.081
Genetic variation in the Estonian population	Estonian	Study-wide	4478	C=0.8707	T=0.1293
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.8731	T=0.1269
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.8533	T=0.1467
KOREAN population from KRGDB	KOREAN	Study-wide	2918	C=0.9931	T=0.0069
Northern Sweden	ACPOP	Study-wide	598	C=0.848	T=0.152
Qatari	Global	Study-wide	216	C=0.875	T=0.125
SGDP_PRJ	Global	Study-wide	120	C=0.425	T=0.575
PharmGKB Aggregated	Global	Study-wide	90	C=0.88	T=0.12
PharmGKB Aggregated	PA151897395	Sub	90	C=0.88	T=0.12
The Danish reference pan genome	Danish	Study-wide	40	C=0.90	T=0.10
Siberian	Global	Study-wide	10	C=0.4	T=0.6

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements

Sequence name	Change
GRCh38.p14 chr 19	NC_000019.10:g.11132746C>A
GRCh38.p14 chr 19	NC_000019.10:g.11132746C>T
GRCh37.p13 chr 19	NC_000019.9:g.11243422C>A
GRCh37.p13 chr 19	NC_000019.9:g.11243422C>T
LDLR RefSeqGene (LRG_274)	NG_009060.1:g.48366C>A
LDLR RefSeqGene (LRG_274)	NG_009060.1:g.48366C>T

Gene: LDLR, low density lipoprotein receptor (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LDLR transcript variant 4	NM_001195800.2:c.*1430=	N/A	3 Prime UTR Variant
LDLR transcript variant 6	NM_001195803.2:c.*1430=	N/A	3 Prime UTR Variant
LDLR transcript variant 2	NM_001195798.2:c.*1430=	N/A	3 Prime UTR Variant
LDLR transcript variant 3	NM_001195799.2:c.*1430=	N/A	3 Prime UTR Variant
LDLR transcript variant 1	NM_000527.5:c.*1430=	N/A	3 Prime UTR Variant
LDLR transcript variant X1	XM_011528010.3:c.*1430=	N/A	3 Prime UTR Variant
LDLR transcript variant X2	XM_047438831.1:c.	N/A	Genic Downstream Transcript Variant

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Allele: A (allele ID: 879856 )

ClinVar Accession	Disease Names	Clinical Significance
RCV001127422.2	Hypercholesterolemia, familial, 1	Uncertain-Significance

Allele: T (allele ID: 349330 )

ClinVar Accession	Disease Names	Clinical Significance
RCV000309993.3	Hypercholesterolemia, familial, 1	Benign

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement	C=	A	T
GRCh38.p14 chr 19	NC_000019.10:g.11132746=	NC_000019.10:g.11132746C>A	NC_000019.10:g.11132746C>T
GRCh37.p13 chr 19	NC_000019.9:g.11243422=	NC_000019.9:g.11243422C>A	NC_000019.9:g.11243422C>T
LDLR RefSeqGene (LRG_274)	NG_009060.1:g.48366=	NG_009060.1:g.48366C>A	NG_009060.1:g.48366C>T
LDLR transcript variant 1	NM_000527.5:c.*1430=	NM_000527.5:c.*1430C>A	NM_000527.5:c.*1430C>T
LDLR transcript variant 1	NM_000527.4:c.*1430=	NM_000527.4:c.*1430C>A	NM_000527.4:c.*1430C>T
LDLR transcript variant 2	NM_001195798.2:c.*1430=	NM_001195798.2:c.*1430C>A	NM_001195798.2:c.*1430C>T
LDLR transcript variant 2	NM_001195798.1:c.*1430=	NM_001195798.1:c.*1430C>A	NM_001195798.1:c.*1430C>T
LDLR transcript variant 3	NM_001195799.2:c.*1430=	NM_001195799.2:c.*1430C>A	NM_001195799.2:c.*1430C>T
LDLR transcript variant 3	NM_001195799.1:c.*1430=	NM_001195799.1:c.*1430C>A	NM_001195799.1:c.*1430C>T
LDLR transcript variant 4	NM_001195800.2:c.*1430=	NM_001195800.2:c.*1430C>A	NM_001195800.2:c.*1430C>T
LDLR transcript variant 4	NM_001195800.1:c.*1430=	NM_001195800.1:c.*1430C>A	NM_001195800.1:c.*1430C>T
LDLR transcript variant 6	NM_001195803.2:c.*1430=	NM_001195803.2:c.*1430C>A	NM_001195803.2:c.*1430C>T
LDLR transcript variant 6	NM_001195803.1:c.*1430=	NM_001195803.1:c.*1430C>A	NM_001195803.1:c.*1430C>T
LDLR transcript variant X1	XM_011528010.3:c.*1430=	XM_011528010.3:c.*1430C>A	XM_011528010.3:c.*1430C>T
LDLR transcript variant X1	XM_011528010.2:c.*1430=	XM_011528010.2:c.*1430C>A	XM_011528010.2:c.*1430C>T
LDLR transcript variant X1	XM_011528010.1:c.*1430=	XM_011528010.1:c.*1430C>A	XM_011528010.1:c.*1430C>T
LDLR transcript variant 5	NM_001195802.1:c.*1430=	NM_001195802.1:c.*1430C>A	NM_001195802.1:c.*1430C>T

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

47 SubSNP, 18 Frequency, 2 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	BCM_SSAHASNP	ss10934082	Jul 11, 2003 (116)
2	PARC	ss23144379	Sep 20, 2004 (126)
3	HGSV	ss78693891	Dec 07, 2007 (129)
4	PHARMGKB_PARC	ss84140926	Dec 14, 2007 (130)
5	ILLUMINA-UK	ss117640189	Dec 01, 2009 (131)
6	COMPLETE_GENOMICS	ss167807764	Jul 04, 2010 (132)
7	1000GENOMES	ss228042704	Jul 14, 2010 (132)
8	1000GENOMES	ss237603719	Jul 15, 2010 (132)
9	BL	ss255492668	May 09, 2011 (134)
10	GMI	ss287345876	Apr 25, 2013 (138)
11	PJP	ss292212677	May 09, 2011 (134)
12	TISHKOFF	ss565856302	Apr 25, 2013 (138)
13	SSMP	ss661712610	Apr 25, 2013 (138)
14	1000GENOMES	ss1362372947	Aug 21, 2014 (142)
15	DDI	ss1428337458	Apr 01, 2015 (144)
16	EVA_GENOME_DK	ss1578557931	Apr 01, 2015 (144)
17	EVA_UK10K_ALSPAC	ss1637574657	Apr 01, 2015 (144)
18	EVA_UK10K_TWINSUK	ss1680568690	Apr 01, 2015 (144)
19	WEILL_CORNELL_DGM	ss1937576782	Feb 12, 2016 (147)
20	JJLAB	ss2029561346	Sep 14, 2016 (149)
21	USC_VALOUEV	ss2158084497	Dec 20, 2016 (150)
22	HUMAN_LONGEVITY	ss2224331114	Dec 20, 2016 (150)
23	GRF	ss2702688589	Nov 08, 2017 (151)
24	GNOMAD	ss2960524610	Nov 08, 2017 (151)
25	SWEGEN	ss3017108700	Nov 08, 2017 (151)
26	BIOINF_KMB_FNS_UNIBA	ss3028613715	Nov 08, 2017 (151)
27	CSHL	ss3352200801	Nov 08, 2017 (151)
28	EGCUT_WGS	ss3683940037	Jul 13, 2019 (153)
29	EVA_DECODE	ss3702355820	Jul 13, 2019 (153)
30	EVA_DECODE	ss3702355821	Jul 13, 2019 (153)
31	ACPOP	ss3742859595	Jul 13, 2019 (153)
32	EVA	ss3755817884	Jul 13, 2019 (153)
33	KHV_HUMAN_GENOMES	ss3821072642	Jul 13, 2019 (153)
34	EVA	ss3835354372	Apr 27, 2020 (154)
35	SGDP_PRJ	ss3887777960	Apr 27, 2020 (154)
36	KRGDB	ss3937750845	Apr 27, 2020 (154)
37	TOPMED	ss5068140595	Apr 27, 2021 (155)
38	TOMMO_GENOMICS	ss5226770808	Apr 27, 2021 (155)
39	1000G_HIGH_COVERAGE	ss5306514793	Oct 16, 2022 (156)
40	HUGCELL_USP	ss5499140838	Oct 16, 2022 (156)
41	1000G_HIGH_COVERAGE	ss5611921527	Oct 16, 2022 (156)
42	SANFORD_IMAGENETICS	ss5661987410	Oct 16, 2022 (156)
43	TOMMO_GENOMICS	ss5785060890	Oct 16, 2022 (156)
44	EVA	ss5840262387	Oct 16, 2022 (156)
45	EVA	ss5852207030	Oct 16, 2022 (156)
46	EVA	ss5927318994	Oct 16, 2022 (156)
47	EVA	ss5953409267	Oct 16, 2022 (156)
48	1000Genomes	NC_000019.9 - 11243422	Oct 12, 2018 (152)
49	1000Genomes_30x	NC_000019.10 - 11132746	Oct 16, 2022 (156)
50	The Avon Longitudinal Study of Parents and Children	NC_000019.9 - 11243422	Oct 12, 2018 (152)
51	Genetic variation in the Estonian population	NC_000019.9 - 11243422	Oct 12, 2018 (152)
52	The Danish reference pan genome	NC_000019.9 - 11243422	Apr 27, 2020 (154)
53	gnomAD - Genomes Submission ignored due to conflicting rows: Row 534225465 (NC_000019.10:11132745:C:A 17/139272) Row 534225466 (NC_000019.10:11132745:C:T 18225/139244)	-	Apr 27, 2021 (155)
54	gnomAD - Genomes Submission ignored due to conflicting rows: Row 534225465 (NC_000019.10:11132745:C:A 17/139272) Row 534225466 (NC_000019.10:11132745:C:T 18225/139244)	-	Apr 27, 2021 (155)
55	KOREAN population from KRGDB	NC_000019.9 - 11243422	Apr 27, 2020 (154)
56	Northern Sweden	NC_000019.9 - 11243422	Jul 13, 2019 (153)
57	PharmGKB Aggregated	NC_000019.10 - 11132746	Apr 27, 2020 (154)
58	Qatari	NC_000019.9 - 11243422	Apr 27, 2020 (154)
59	SGDP_PRJ	NC_000019.9 - 11243422	Apr 27, 2020 (154)
60	Siberian	NC_000019.9 - 11243422	Apr 27, 2020 (154)
61	8.3KJPN	NC_000019.9 - 11243422	Apr 27, 2021 (155)
62	14KJPN	NC_000019.10 - 11132746	Oct 16, 2022 (156)
63	TopMed	NC_000019.10 - 11132746	Apr 27, 2021 (155)
64	UK 10K study - Twins	NC_000019.9 - 11243422	Oct 12, 2018 (152)
65	ALFA	NC_000019.10 - 11132746	Apr 27, 2021 (155)
66	ClinVar	RCV000309993.3	Oct 16, 2022 (156)
67	ClinVar	RCV001127422.2	Oct 16, 2022 (156)

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Associated ID	History Updated (Build)
rs17242690	Mar 11, 2006 (126)
rs58126234	May 24, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss2960524610	NC_000019.9:11243421:C:A	NC_000019.10:11132745:C:A	(self)
RCV001127422.2, 8236216875, ss2224331114, ss3702355820	NC_000019.10:11132745:C:A	NC_000019.10:11132745:C:A	(self)
ss78693891, ss117640189, ss167807764, ss255492668, ss287345876, ss292212677	NC_000019.8:11104421:C:T	NC_000019.10:11132745:C:T	(self)
75751169, 41971729, 29678285, 4743664, 44928239, 16144460, 19618704, 39794940, 10600851, 84740115, 41971729, ss228042704, ss237603719, ss565856302, ss661712610, ss1362372947, ss1428337458, ss1578557931, ss1637574657, ss1680568690, ss1937576782, ss2029561346, ss2158084497, ss2702688589, ss2960524610, ss3017108700, ss3352200801, ss3683940037, ss3742859595, ss3755817884, ss3835354372, ss3887777960, ss3937750845, ss5226770808, ss5661987410, ss5840262387, ss5953409267	NC_000019.9:11243421:C:T	NC_000019.10:11132745:C:T	(self)
RCV000309993.3, 99447462, 5576, 118897994, 283686259, 8236216875, ss2224331114, ss3028613715, ss3702355821, ss3821072642, ss5068140595, ss5306514793, ss5499140838, ss5611921527, ss5785060890, ss5852207030, ss5927318994	NC_000019.10:11132745:C:T	NC_000019.10:11132745:C:T	(self)
ss10934082	NT_011295.10:2506223:C:T	NC_000019.10:11132745:C:T	(self)
ss23144379, ss84140926	NT_011295.11:2506223:C:T	NC_000019.10:11132745:C:T	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs7254521

PMID	Title	Author	Year	Journal
20413733	Combined influence of LDLR and HMGCR sequence variation on lipid-lowering response to simvastatin.	Mangravite LM et al.	2010	Arteriosclerosis, thrombosis, and vascular biology

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:

Select flank length:

Genomic regions, transcripts, and products
Top▲ Help
NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs7254521