Name: rs269
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.

rs269

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr8:19956156 (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: T>A / T>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.270566 (71616/264690, TOPMED)
G=0.16755 (5292/31584, ALFA)
G=0.21594 (6102/28258, 14KJPN) (+ 19 more)
G=0.21826 (3658/16760, 8.3KJPN)
G=0.2883 (1846/6404, 1000G_30x)
G=0.2780 (1392/5008, 1000G)
G=0.1562 (700/4480, Estonian)
G=0.1819 (701/3854, ALSPAC)
G=0.1882 (698/3708, TWINSUK)
G=0.2078 (609/2930, KOREAN)
G=0.3155 (597/1892, HapMap)
G=0.1949 (357/1832, Korea1K)
G=0.182 (182/998, GoNL)
G=0.140 (84/600, NorthernSweden)
G=0.230 (123/534, MGP)
T=0.388 (87/224, SGDP_PRJ)
G=0.222 (48/216, Qatari)
G=0.213 (46/216, Vietnamese)
G=0.24 (20/84, Ancient Sardinia)
G=0.15 (6/40, GENOME_DK)
T=0.50 (8/16, Siberian)
G=0.50 (8/16, Siberian)

Clinical Significance: Reported in ClinVar
Gene : Consequence: LPL : 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	31584	T=0.83245	A=0.00000, G=0.16755	0.705167	0.040274	0.254559	32
European	Sub	26288	T=0.84898	A=0.00000, G=0.15102	0.725502	0.027541	0.246957	10
African	Sub	2734	T=0.6697	A=0.0000, G=0.3303	0.488661	0.149232	0.362107	24
African Others	Sub	98	T=0.62	A=0.00, G=0.38	0.408163	0.163265	0.428571	0
African American	Sub	2636	T=0.6715	A=0.0000, G=0.3285	0.491654	0.14871	0.359636	24
Asian	Sub	72	T=0.89	A=0.00, G=0.11	0.833333	0.055556	0.111111	4
East Asian	Sub	58	T=0.86	A=0.00, G=0.14	0.793103	0.068966	0.137931	3
Other Asian	Sub	14	T=1.00	A=0.00, G=0.00	1.0	0.0	0.0	N/A
Latin American 1	Sub	130	T=0.915	A=0.000, G=0.085	0.861538	0.030769	0.107692	4
Latin American 2	Sub	540	T=0.944	A=0.000, G=0.056	0.907407	0.018519	0.074074	13
South Asian	Sub	86	T=0.91	A=0.00, G=0.09	0.860465	0.046512	0.093023	5
Other	Sub	1734	T=0.7912	A=0.0000, G=0.2088	0.650519	0.068051	0.28143	11

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	T=0.729434	G=0.270566
Allele Frequency Aggregator	Total	Global	31584	T=0.83245	A=0.00000, G=0.16755
Allele Frequency Aggregator	European	Sub	26288	T=0.84898	A=0.00000, G=0.15102
Allele Frequency Aggregator	African	Sub	2734	T=0.6697	A=0.0000, G=0.3303
Allele Frequency Aggregator	Other	Sub	1734	T=0.7912	A=0.0000, G=0.2088
Allele Frequency Aggregator	Latin American 2	Sub	540	T=0.944	A=0.000, G=0.056
Allele Frequency Aggregator	Latin American 1	Sub	130	T=0.915	A=0.000, G=0.085
Allele Frequency Aggregator	South Asian	Sub	86	T=0.91	A=0.00, G=0.09
Allele Frequency Aggregator	Asian	Sub	72	T=0.89	A=0.00, G=0.11
14KJPN	JAPANESE	Study-wide	28258	T=0.78406	G=0.21594
8.3KJPN	JAPANESE	Study-wide	16760	T=0.78174	G=0.21826
1000Genomes_30x	Global	Study-wide	6404	T=0.7117	G=0.2883
1000Genomes_30x	African	Sub	1786	T=0.5157	G=0.4843
1000Genomes_30x	Europe	Sub	1266	T=0.7891	G=0.2109
1000Genomes_30x	South Asian	Sub	1202	T=0.8128	G=0.1872
1000Genomes_30x	East Asian	Sub	1170	T=0.7504	G=0.2496
1000Genomes_30x	American	Sub	980	T=0.799	G=0.201
1000Genomes	Global	Study-wide	5008	T=0.7220	G=0.2780
1000Genomes	African	Sub	1322	T=0.5295	G=0.4705
1000Genomes	East Asian	Sub	1008	T=0.7540	G=0.2460
1000Genomes	Europe	Sub	1006	T=0.8012	G=0.1988
1000Genomes	South Asian	Sub	978	T=0.812	G=0.188
1000Genomes	American	Sub	694	T=0.801	G=0.199
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.8438	G=0.1562
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.8181	G=0.1819
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.8118	G=0.1882
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.7922	G=0.2078
HapMap	Global	Study-wide	1892	T=0.6845	G=0.3155
HapMap	American	Sub	770	T=0.775	G=0.225
HapMap	African	Sub	692	T=0.533	G=0.467
HapMap	Asian	Sub	254	T=0.780	G=0.220
HapMap	Europe	Sub	176	T=0.744	G=0.256
Korean Genome Project	KOREAN	Study-wide	1832	T=0.8051	G=0.1949
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.818	G=0.182
Northern Sweden	ACPOP	Study-wide	600	T=0.860	G=0.140
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	T=0.770	G=0.230
SGDP_PRJ	Global	Study-wide	224	T=0.388	G=0.612
Qatari	Global	Study-wide	216	T=0.778	G=0.222
A Vietnamese Genetic Variation Database	Global	Study-wide	216	T=0.787	G=0.213
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	84	T=0.76	G=0.24
The Danish reference pan genome	Danish	Study-wide	40	T=0.85	G=0.15
Siberian	Global	Study-wide	16	T=0.50	G=0.50

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 8	NC_000008.11:g.19956156T>A
GRCh38.p14 chr 8	NC_000008.11:g.19956156T>G
GRCh37.p13 chr 8	NC_000008.10:g.19813667T>A
GRCh37.p13 chr 8	NC_000008.10:g.19813667T>G
LPL RefSeqGene (LRG_1298)	NG_008855.2:g.59440T>A
LPL RefSeqGene (LRG_1298)	NG_008855.2:g.59440T>G

Gene: LPL, lipoprotein lipase (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LPL transcript	NM_000237.3:c.1018+73T>A	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.

Allele: G (allele ID: 1278807 )

ClinVar Accession	Disease Names	Clinical Significance
RCV001709424.1	not provided	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	T=	A	G
GRCh38.p14 chr 8	NC_000008.11:g.19956156=	NC_000008.11:g.19956156T>A	NC_000008.11:g.19956156T>G
GRCh37.p13 chr 8	NC_000008.10:g.19813667=	NC_000008.10:g.19813667T>A	NC_000008.10:g.19813667T>G
LPL RefSeqGene (LRG_1298)	NG_008855.2:g.59440=	NG_008855.2:g.59440T>A	NG_008855.2:g.59440T>G
LPL transcript	NM_000237.2:c.1018+73=	NM_000237.2:c.1018+73T>A	NM_000237.2:c.1018+73T>G
LPL transcript	NM_000237.3:c.1018+73=	NM_000237.3:c.1018+73T>A	NM_000237.3:c.1018+73T>G

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#.

89 SubSNP, 23 Frequency, 1 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	DEBNICK	ss269	Sep 19, 2000 (36)
2	YUSUKE	ss2990800	Jun 15, 2001 (96)
3	IMCJ-GDT	ss16343021	Feb 27, 2004 (120)
4	PERLEGEN	ss23712757	Sep 20, 2004 (123)
5	ILLUMINA	ss75116026	Dec 07, 2007 (129)
6	HGSV	ss78939034	Dec 07, 2007 (129)
7	BGI	ss104512509	Dec 01, 2009 (131)
8	ILLUMINA-UK	ss115864228	Feb 14, 2009 (130)
9	KRIBB_YJKIM	ss119336840	Dec 01, 2009 (131)
10	COMPLETE_GENOMICS	ss162224024	Jul 04, 2010 (132)
11	COMPLETE_GENOMICS	ss164131628	Jul 04, 2010 (132)
12	ILLUMINA	ss173430888	Jul 04, 2010 (132)
13	BUSHMAN	ss198888107	Jul 04, 2010 (132)
14	1000GENOMES	ss223585634	Jul 14, 2010 (132)
15	1000GENOMES	ss234352470	Jul 15, 2010 (132)
16	1000GENOMES	ss241227294	Jul 15, 2010 (132)
17	BL	ss254171422	May 09, 2011 (134)
18	GMI	ss279724015	May 04, 2012 (137)
19	ILLUMINA	ss410878537	Sep 17, 2011 (135)
20	ILLUMINA	ss483085706	May 04, 2012 (137)
21	ILLUMINA	ss485584679	May 04, 2012 (137)
22	ILLUMINA	ss535239967	Sep 08, 2015 (146)
23	TISHKOFF	ss560600112	Apr 25, 2013 (138)
24	SSMP	ss655035552	Apr 25, 2013 (138)
25	ILLUMINA	ss780145613	Aug 21, 2014 (142)
26	ILLUMINA	ss781986271	Aug 21, 2014 (142)
27	ILLUMINA	ss835629090	Aug 21, 2014 (142)
28	EVA-GONL	ss985272619	Aug 21, 2014 (142)
29	JMKIDD_LAB	ss1075340006	Aug 21, 2014 (142)
30	1000GENOMES	ss1328915153	Aug 21, 2014 (142)
31	DDI	ss1431441577	Apr 01, 2015 (144)
32	EVA_GENOME_DK	ss1582593753	Apr 01, 2015 (144)
33	EVA_DECODE	ss1594862273	Apr 01, 2015 (144)
34	EVA_UK10K_ALSPAC	ss1620133704	Apr 01, 2015 (144)
35	EVA_UK10K_TWINSUK	ss1663127737	Apr 01, 2015 (144)
36	EVA_MGP	ss1711194708	Apr 01, 2015 (144)
37	EVA_SVP	ss1713021091	Apr 01, 2015 (144)
38	HAMMER_LAB	ss1805432784	Sep 08, 2015 (146)
39	WEILL_CORNELL_DGM	ss1928562370	Feb 12, 2016 (147)
40	GENOMED	ss1970929934	Jul 19, 2016 (147)
41	JJLAB	ss2024980550	Sep 14, 2016 (149)
42	USC_VALOUEV	ss2153202013	Dec 20, 2016 (150)
43	HUMAN_LONGEVITY	ss2301287951	Dec 20, 2016 (150)
44	SYSTEMSBIOZJU	ss2626975145	Nov 08, 2017 (151)
45	ILLUMINA	ss2634720446	Nov 08, 2017 (151)
46	GRF	ss2708962521	Nov 08, 2017 (151)
47	GNOMAD	ss2864092863	Nov 08, 2017 (151)
48	AFFY	ss2986076178	Nov 08, 2017 (151)
49	SWEGEN	ss3002804434	Nov 08, 2017 (151)
50	BIOINF_KMB_FNS_UNIBA	ss3026281100	Nov 08, 2017 (151)
51	CSHL	ss3348082025	Nov 08, 2017 (151)
52	ILLUMINA	ss3630013640	Oct 12, 2018 (152)
53	ILLUMINA	ss3632620993	Oct 12, 2018 (152)
54	ILLUMINA	ss3638748369	Oct 12, 2018 (152)
55	ILLUMINA	ss3642618966	Oct 12, 2018 (152)
56	ILLUMINA	ss3643680167	Oct 12, 2018 (152)
57	OMUKHERJEE_ADBS	ss3646373020	Oct 12, 2018 (152)
58	EGCUT_WGS	ss3670484470	Jul 13, 2019 (153)
59	EVA_DECODE	ss3721555443	Jul 13, 2019 (153)
60	ACPOP	ss3735467035	Jul 13, 2019 (153)
61	EVA	ss3767717756	Jul 13, 2019 (153)
62	PACBIO	ss3786087363	Jul 13, 2019 (153)
63	PACBIO	ss3791353771	Jul 13, 2019 (153)
64	PACBIO	ss3796234938	Jul 13, 2019 (153)
65	KHV_HUMAN_GENOMES	ss3810881221	Jul 13, 2019 (153)
66	EVA	ss3831054900	Apr 26, 2020 (154)
67	SGDP_PRJ	ss3869436721	Apr 26, 2020 (154)
68	KRGDB	ss3916862542	Apr 26, 2020 (154)
69	KOGIC	ss3963402175	Apr 26, 2020 (154)
70	FSA-LAB	ss3984393695	Apr 27, 2021 (155)
71	FSA-LAB	ss3984393696	Apr 27, 2021 (155)
72	EVA	ss3985347112	Apr 27, 2021 (155)
73	EVA	ss3986415478	Apr 27, 2021 (155)
74	EVA	ss4017379940	Apr 27, 2021 (155)
75	TOPMED	ss4778093065	Apr 27, 2021 (155)
76	TOMMO_GENOMICS	ss5187654422	Apr 27, 2021 (155)
77	1000G_HIGH_COVERAGE	ss5276330179	Oct 14, 2022 (156)
78	EVA	ss5315316835	Oct 14, 2022 (156)
79	EVA	ss5379642208	Oct 14, 2022 (156)
80	HUGCELL_USP	ss5472980793	Oct 14, 2022 (156)
81	1000G_HIGH_COVERAGE	ss5566254049	Oct 14, 2022 (156)
82	EVA	ss5624176081	Oct 14, 2022 (156)
83	SANFORD_IMAGENETICS	ss5644923848	Oct 14, 2022 (156)
84	TOMMO_GENOMICS	ss5729271025	Oct 14, 2022 (156)
85	YY_MCH	ss5809516736	Oct 14, 2022 (156)
86	EVA	ss5830224468	Oct 14, 2022 (156)
87	EVA	ss5848702265	Oct 14, 2022 (156)
88	EVA	ss5888021526	Oct 14, 2022 (156)
89	EVA	ss5974104344	Oct 14, 2022 (156)
90	1000Genomes	NC_000008.10 - 19813667	Oct 12, 2018 (152)
91	1000Genomes_30x	NC_000008.11 - 19956156	Oct 14, 2022 (156)
92	The Avon Longitudinal Study of Parents and Children	NC_000008.10 - 19813667	Oct 12, 2018 (152)
93	Genetic variation in the Estonian population	NC_000008.10 - 19813667	Oct 12, 2018 (152)
94	The Danish reference pan genome	NC_000008.10 - 19813667	Apr 26, 2020 (154)
95	gnomAD - Genomes Submission ignored due to conflicting rows: Row 289194909 (NC_000008.11:19956155:T:A 1/140192) Row 289194910 (NC_000008.11:19956155:T:G 36916/140168)	-	Apr 27, 2021 (155)
96	gnomAD - Genomes Submission ignored due to conflicting rows: Row 289194909 (NC_000008.11:19956155:T:A 1/140192) Row 289194910 (NC_000008.11:19956155:T:G 36916/140168)	-	Apr 27, 2021 (155)
97	Genome of the Netherlands Release 5	NC_000008.10 - 19813667	Apr 26, 2020 (154)
98	HapMap	NC_000008.11 - 19956156	Apr 26, 2020 (154)
99	KOREAN population from KRGDB	NC_000008.10 - 19813667	Apr 26, 2020 (154)
100	Korean Genome Project	NC_000008.11 - 19956156	Apr 26, 2020 (154)
101	Medical Genome Project healthy controls from Spanish population	NC_000008.10 - 19813667	Apr 26, 2020 (154)
102	Northern Sweden	NC_000008.10 - 19813667	Jul 13, 2019 (153)
103	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000008.10 - 19813667	Apr 27, 2021 (155)
104	Qatari	NC_000008.10 - 19813667	Apr 26, 2020 (154)
105	SGDP_PRJ	NC_000008.10 - 19813667	Apr 26, 2020 (154)
106	Siberian	NC_000008.10 - 19813667	Apr 26, 2020 (154)
107	8.3KJPN	NC_000008.10 - 19813667	Apr 27, 2021 (155)
108	14KJPN	NC_000008.11 - 19956156	Oct 14, 2022 (156)
109	TopMed	NC_000008.11 - 19956156	Apr 27, 2021 (155)
110	UK 10K study - Twins	NC_000008.10 - 19813667	Oct 12, 2018 (152)
111	A Vietnamese Genetic Variation Database	NC_000008.10 - 19813667	Jul 13, 2019 (153)
112	ALFA	NC_000008.11 - 19956156	Apr 27, 2021 (155)
113	ClinVar	RCV001709424.1	Oct 14, 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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
10676160304	NC_000008.11:19956155:T:A	NC_000008.11:19956155:T:A	(self)
ss78939034, ss115864228, ss162224024, ss164131628, ss198888107, ss254171422, ss279724015, ss410878537, ss485584679, ss1594862273, ss1713021091, ss3643680167	NC_000008.9:19857946:T:G	NC_000008.11:19956155:T:G	(self)
41009896, 22797097, 16222718, 8758691, 10186935, 24039936, 310468, 8751900, 573039, 10604300, 21453701, 5718367, 45623729, 22797097, 5083468, ss223585634, ss234352470, ss241227294, ss483085706, ss535239967, ss560600112, ss655035552, ss780145613, ss781986271, ss835629090, ss985272619, ss1075340006, ss1328915153, ss1431441577, ss1582593753, ss1620133704, ss1663127737, ss1711194708, ss1805432784, ss1928562370, ss1970929934, ss2024980550, ss2153202013, ss2626975145, ss2634720446, ss2708962521, ss2864092863, ss2986076178, ss3002804434, ss3348082025, ss3630013640, ss3632620993, ss3638748369, ss3642618966, ss3646373020, ss3670484470, ss3735467035, ss3767717756, ss3786087363, ss3791353771, ss3796234938, ss3831054900, ss3869436721, ss3916862542, ss3984393695, ss3984393696, ss3985347112, ss3986415478, ss4017379940, ss5187654422, ss5315316835, ss5379642208, ss5624176081, ss5644923848, ss5830224468, ss5848702265, ss5974104344	NC_000008.10:19813666:T:G	NC_000008.11:19956155:T:G	(self)
RCV001709424.1, 53779984, 3580982, 19780176, 63108129, 615470625, 10676160304, ss2301287951, ss3026281100, ss3721555443, ss3810881221, ss3963402175, ss4778093065, ss5276330179, ss5472980793, ss5566254049, ss5729271025, ss5809516736, ss5888021526	NC_000008.11:19956155:T:G	NC_000008.11:19956155:T:G	(self)
ss269, ss2990800, ss16343021, ss23712757, ss75116026, ss104512509, ss119336840, ss173430888	NT_167187.1:7671812:T:G	NC_000008.11:19956155:T:G	(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 rs269

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

rs269