Name: rs4709437
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.

rs4709437

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:160504823 (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: G>A / G>C / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.273539 (72403/264690, TOPMED)
T=0.260661 (36466/139898, GnomAD)
G=0.47257 (13354/28258, 14KJPN) (+ 16 more)
G=0.47416 (7947/16760, 8.3KJPN)
T=0.15741 (2125/13500, ALFA)
T=0.3362 (2153/6404, 1000G_30x)
T=0.3389 (1697/5008, 1000G)
T=0.3161 (1416/4480, Estonian)
T=0.3033 (1169/3854, ALSPAC)
T=0.2967 (1100/3708, TWINSUK)
G=0.4584 (1343/2930, KOREAN)
G=0.4645 (851/1832, Korea1K)
T=0.269 (268/998, GoNL)
T=0.338 (203/600, NorthernSweden)
G=0.332 (103/310, SGDP_PRJ)
T=0.227 (49/216, Qatari)
T=0.491 (104/212, Vietnamese)
T=0.33 (13/40, GENOME_DK)
G=0.19 (7/36, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LPAL2 : Intron Variant
Publications: 0 citations
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: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	13500	G=0.84259	C=0.00000, T=0.15741
European	Sub	10456	G=0.80480	C=0.00000, T=0.19520
African	Sub	2254	G=0.9911	C=0.0000, T=0.0089
African Others	Sub	90	G=1.00	C=0.00, T=0.00
African American	Sub	2164	G=0.9908	C=0.0000, T=0.0092
Asian	Sub	26	G=0.85	C=0.00, T=0.15
East Asian	Sub	22	G=0.91	C=0.00, T=0.09
Other Asian	Sub	4	G=0.5	C=0.0, T=0.5
Latin American 1	Sub	72	G=1.00	C=0.00, T=0.00
Latin American 2	Sub	198	G=1.000	C=0.000, T=0.000
South Asian	Sub	34	G=0.94	C=0.00, T=0.06
Other	Sub	460	G=0.874	C=0.000, T=0.126

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	G=0.726461	T=0.273539
gnomAD - Genomes	Global	Study-wide	139898	G=0.739339	T=0.260661
gnomAD - Genomes	European	Sub	75754	G=0.70386	T=0.29614
gnomAD - Genomes	African	Sub	41936	G=0.86663	T=0.13337
gnomAD - Genomes	American	Sub	13636	G=0.63318	T=0.36682
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	G=0.6757	T=0.3243
gnomAD - Genomes	East Asian	Sub	3106	G=0.4524	T=0.5476
gnomAD - Genomes	Other	Sub	2148	G=0.6927	T=0.3073
14KJPN	JAPANESE	Study-wide	28258	G=0.47257	T=0.52743
8.3KJPN	JAPANESE	Study-wide	16760	G=0.47416	T=0.52584
Allele Frequency Aggregator	Total	Global	13500	G=0.84259	C=0.00000, T=0.15741
Allele Frequency Aggregator	European	Sub	10456	G=0.80480	C=0.00000, T=0.19520
Allele Frequency Aggregator	African	Sub	2254	G=0.9911	C=0.0000, T=0.0089
Allele Frequency Aggregator	Other	Sub	460	G=0.874	C=0.000, T=0.126
Allele Frequency Aggregator	Latin American 2	Sub	198	G=1.000	C=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	72	G=1.00	C=0.00, T=0.00
Allele Frequency Aggregator	South Asian	Sub	34	G=0.94	C=0.00, T=0.06
Allele Frequency Aggregator	Asian	Sub	26	G=0.85	C=0.00, T=0.15
1000Genomes_30x	Global	Study-wide	6404	G=0.6638	T=0.3362
1000Genomes_30x	African	Sub	1786	G=0.8813	T=0.1187
1000Genomes_30x	Europe	Sub	1266	G=0.7148	T=0.2852
1000Genomes_30x	South Asian	Sub	1202	G=0.5707	T=0.4293
1000Genomes_30x	East Asian	Sub	1170	G=0.4538	T=0.5462
1000Genomes_30x	American	Sub	980	G=0.566	T=0.434
1000Genomes	Global	Study-wide	5008	G=0.6611	T=0.3389
1000Genomes	African	Sub	1322	G=0.8865	T=0.1135
1000Genomes	East Asian	Sub	1008	G=0.4524	T=0.5476
1000Genomes	Europe	Sub	1006	G=0.7276	T=0.2724
1000Genomes	South Asian	Sub	978	G=0.577	T=0.423
1000Genomes	American	Sub	694	G=0.558	T=0.442
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.6839	T=0.3161
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.6967	T=0.3033
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.7033	T=0.2967
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.4584	A=0.0000, C=0.0000, T=0.5416
Korean Genome Project	KOREAN	Study-wide	1832	G=0.4645	T=0.5355
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.731	T=0.269
Northern Sweden	ACPOP	Study-wide	600	G=0.662	T=0.338
SGDP_PRJ	Global	Study-wide	310	G=0.332	T=0.668
Qatari	Global	Study-wide	216	G=0.773	T=0.227
A Vietnamese Genetic Variation Database	Global	Study-wide	212	G=0.509	T=0.491
The Danish reference pan genome	Danish	Study-wide	40	G=0.68	T=0.33
Siberian	Global	Study-wide	36	G=0.19	T=0.81

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 6	NC_000006.12:g.160504823G>A
GRCh38.p14 chr 6	NC_000006.12:g.160504823G>C
GRCh38.p14 chr 6	NC_000006.12:g.160504823G>T
GRCh37.p13 chr 6	NC_000006.11:g.160925855G>A
GRCh37.p13 chr 6	NC_000006.11:g.160925855G>C
GRCh37.p13 chr 6	NC_000006.11:g.160925855G>T

Gene: LPAL2, lipoprotein(a) like 2, pseudogene (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LPAL2 transcript variant 1	NR_028092.1:n.	N/A	Intron Variant
LPAL2 transcript variant 2	NR_028093.1:n.	N/A	Intron 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.

Not Reported in ClinVar

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	G=	A	C	T
GRCh38.p14 chr 6	NC_000006.12:g.160504823=	NC_000006.12:g.160504823G>A	NC_000006.12:g.160504823G>C	NC_000006.12:g.160504823G>T
GRCh37.p13 chr 6	NC_000006.11:g.160925855=	NC_000006.11:g.160925855G>A	NC_000006.11:g.160925855G>C	NC_000006.11:g.160925855G>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#.

66 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WI_SSAHASNP	ss6488999	Feb 20, 2003 (111)
2	WI_SSAHASNP	ss11154899	Jul 11, 2003 (126)
3	SC_SNP	ss12570455	Aug 26, 2003 (126)
4	SC_SNP	ss12809268	Dec 05, 2003 (126)
5	SSAHASNP	ss22401931	Apr 05, 2004 (126)
6	ABI	ss42660246	Mar 11, 2006 (126)
7	HUMANGENOME_JCVI	ss98557717	Feb 06, 2009 (130)
8	ENSEMBL	ss142719630	Dec 01, 2009 (131)
9	GMI	ss157827711	Dec 01, 2009 (131)
10	COMPLETE_GENOMICS	ss162964453	Jul 04, 2010 (132)
11	BCM-HGSC-SUB	ss207660584	Jul 04, 2010 (132)
12	1000GENOMES	ss222795953	Jul 14, 2010 (132)
13	1000GENOMES	ss233768613	Jul 15, 2010 (132)
14	1000GENOMES	ss240766015	Jul 15, 2010 (132)
15	GMI	ss279105667	May 04, 2012 (137)
16	GMI	ss285540692	Apr 25, 2013 (138)
17	PJP	ss293775609	May 09, 2011 (134)
18	TISHKOFF	ss559669733	Apr 25, 2013 (138)
19	SSMP	ss654012934	Apr 25, 2013 (138)
20	EVA-GONL	ss983731342	Aug 21, 2014 (142)
21	JMKIDD_LAB	ss1074208696	Aug 21, 2014 (142)
22	1000GENOMES	ss1323152871	Aug 21, 2014 (142)
23	DDI	ss1430960107	Apr 01, 2015 (144)
24	EVA_GENOME_DK	ss1581985036	Apr 01, 2015 (144)
25	EVA_DECODE	ss1593307929	Apr 01, 2015 (144)
26	EVA_UK10K_ALSPAC	ss1617172559	Apr 01, 2015 (144)
27	EVA_UK10K_TWINSUK	ss1660166592	Apr 01, 2015 (144)
28	WEILL_CORNELL_DGM	ss1926973617	Feb 12, 2016 (147)
29	GENOMED	ss1970576395	Jul 19, 2016 (147)
30	JJLAB	ss2024153041	Sep 14, 2016 (149)
31	USC_VALOUEV	ss2152346232	Dec 20, 2016 (150)
32	HUMAN_LONGEVITY	ss2290217572	Dec 20, 2016 (150)
33	SYSTEMSBIOZJU	ss2626566737	Nov 08, 2017 (151)
34	GRF	ss2707985273	Nov 08, 2017 (151)
35	GNOMAD	ss2847602710	Nov 08, 2017 (151)
36	SWEGEN	ss3000301226	Nov 08, 2017 (151)
37	BIOINF_KMB_FNS_UNIBA	ss3025867592	Nov 08, 2017 (151)
38	CSHL	ss3347329826	Nov 08, 2017 (151)
39	URBANLAB	ss3648515437	Oct 12, 2018 (152)
40	EGCUT_WGS	ss3668241654	Jul 13, 2019 (153)
41	EVA_DECODE	ss3718710840	Jul 13, 2019 (153)
42	ACPOP	ss3734176907	Jul 13, 2019 (153)
43	EVA	ss3765941323	Jul 13, 2019 (153)
44	KHV_HUMAN_GENOMES	ss3809104293	Jul 13, 2019 (153)
45	EVA	ss3830305597	Apr 26, 2020 (154)
46	EVA	ss3838637066	Apr 26, 2020 (154)
47	EVA	ss3844087194	Apr 26, 2020 (154)
48	SGDP_PRJ	ss3866174789	Apr 26, 2020 (154)
49	KRGDB	ss3913165636	Apr 26, 2020 (154)
50	KOGIC	ss3960498284	Apr 26, 2020 (154)
51	TOPMED	ss4729339500	Apr 26, 2021 (155)
52	TOMMO_GENOMICS	ss5180913466	Apr 26, 2021 (155)
53	1000G_HIGH_COVERAGE	ss5271123510	Oct 13, 2022 (156)
54	EVA	ss5370418971	Oct 13, 2022 (156)
55	HUGCELL_USP	ss5468498169	Oct 13, 2022 (156)
56	EVA	ss5508785361	Oct 13, 2022 (156)
57	1000G_HIGH_COVERAGE	ss5558447120	Oct 13, 2022 (156)
58	SANFORD_IMAGENETICS	ss5641935366	Oct 13, 2022 (156)
59	TOMMO_GENOMICS	ss5720080450	Oct 13, 2022 (156)
60	YY_MCH	ss5808149317	Oct 13, 2022 (156)
61	EVA	ss5843292624	Oct 13, 2022 (156)
62	EVA	ss5855675048	Oct 13, 2022 (156)
63	EVA	ss5886847236	Oct 13, 2022 (156)
64	EVA	ss5970996880	Oct 13, 2022 (156)
65	EVA	ss5970996881	Oct 13, 2022 (156)
66	EVA	ss5980404406	Oct 13, 2022 (156)
67	1000Genomes	NC_000006.11 - 160925855	Oct 12, 2018 (152)
68	1000Genomes_30x	NC_000006.12 - 160504823	Oct 13, 2022 (156)
69	The Avon Longitudinal Study of Parents and Children	NC_000006.11 - 160925855	Oct 12, 2018 (152)
70	Genetic variation in the Estonian population	NC_000006.11 - 160925855	Oct 12, 2018 (152)
71	The Danish reference pan genome	NC_000006.11 - 160925855	Apr 26, 2020 (154)
72	gnomAD - Genomes	NC_000006.12 - 160504823	Apr 26, 2021 (155)
73	Genome of the Netherlands Release 5	NC_000006.11 - 160925855	Apr 26, 2020 (154)
74	KOREAN population from KRGDB	NC_000006.11 - 160925855	Apr 26, 2020 (154)
75	Korean Genome Project	NC_000006.12 - 160504823	Apr 26, 2020 (154)
76	Northern Sweden	NC_000006.11 - 160925855	Jul 13, 2019 (153)
77	Qatari	NC_000006.11 - 160925855	Apr 26, 2020 (154)
78	SGDP_PRJ	NC_000006.11 - 160925855	Apr 26, 2020 (154)
79	Siberian	NC_000006.11 - 160925855	Apr 26, 2020 (154)
80	8.3KJPN	NC_000006.11 - 160925855	Apr 26, 2021 (155)
81	14KJPN	NC_000006.12 - 160504823	Oct 13, 2022 (156)
82	TopMed	NC_000006.12 - 160504823	Apr 26, 2021 (155)
83	UK 10K study - Twins	NC_000006.11 - 160925855	Oct 12, 2018 (152)
84	A Vietnamese Genetic Variation Database	NC_000006.11 - 160925855	Jul 13, 2019 (153)
85	ALFA	NC_000006.12 - 160504823	Apr 26, 2021 (155)

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)
rs7381816	Mar 11, 2006 (126)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
20343030, ss3913165636	NC_000006.11:160925854:G:A	NC_000006.12:160504822:G:A	(self)
20343030, ss3913165636	NC_000006.11:160925854:G:C	NC_000006.12:160504822:G:C	(self)
348309902	NC_000006.12:160504822:G:C	NC_000006.12:160504822:G:C	(self)
ss162964453, ss207660584, ss279105667, ss285540692, ss293775609, ss1593307929	NC_000006.10:160845844:G:T	NC_000006.12:160504822:G:T	(self)
35055359, 19551155, 13979902, 8149975, 8700529, 20343030, 7461772, 9015547, 18191769, 4862586, 38882773, 19551155, 4350778, ss222795953, ss233768613, ss240766015, ss559669733, ss654012934, ss983731342, ss1074208696, ss1323152871, ss1430960107, ss1581985036, ss1617172559, ss1660166592, ss1926973617, ss1970576395, ss2024153041, ss2152346232, ss2626566737, ss2707985273, ss2847602710, ss3000301226, ss3347329826, ss3668241654, ss3734176907, ss3765941323, ss3830305597, ss3838637066, ss3866174789, ss3913165636, ss5180913466, ss5370418971, ss5508785361, ss5641935366, ss5843292624, ss5970996880, ss5970996881, ss5980404406	NC_000006.11:160925854:G:T	NC_000006.12:160504822:G:T	(self)
45973055, 247448344, 16876285, 53917554, 566717058, 348309902, ss2290217572, ss3025867592, ss3648515437, ss3718710840, ss3809104293, ss3844087194, ss3960498284, ss4729339500, ss5271123510, ss5468498169, ss5558447120, ss5720080450, ss5808149317, ss5855675048, ss5886847236	NC_000006.12:160504822:G:T	NC_000006.12:160504822:G:T	(self)
ss11154899, ss12570455, ss22401931	NT_007422.12:3213195:G:T	NC_000006.12:160504822:G:T	(self)
ss6488999, ss12809268, ss42660246, ss98557717, ss142719630, ss157827711	NT_025741.15:65095311:G:T	NC_000006.12:160504822:G:T	(self)

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

No publications for rs4709437

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs4709437