Name: rs1517336
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.

rs1517336

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:168296426 (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: A>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.409766 (108461/264690, TOPMED)
G=0.428770 (60027/139998, GnomAD)
G=0.45514 (42859/94166, ALFA) (+ 19 more)
G=0.35267 (9965/28256, 14KJPN)
G=0.35095 (5882/16760, 8.3KJPN)
G=0.3701 (2370/6404, 1000G_30x)
G=0.3692 (1849/5008, 1000G)
G=0.4737 (2122/4480, Estonian)
G=0.4914 (1894/3854, ALSPAC)
G=0.4951 (1836/3708, TWINSUK)
G=0.3744 (1097/2930, KOREAN)
G=0.3672 (763/2078, HGDP_Stanford)
G=0.3407 (644/1890, HapMap)
G=0.3543 (649/1832, Korea1K)
G=0.474 (473/998, GoNL)
A=0.465 (279/600, NorthernSweden)
A=0.401 (126/314, SGDP_PRJ)
G=0.333 (72/216, Qatari)
G=0.356 (77/216, Vietnamese)
G=0.42 (17/40, GENOME_DK)
A=0.42 (15/36, Siberian)
A=0.3 (2/6, Ancient Sardinia)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: None
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	94166	A=0.54486	G=0.45514
European	Sub	78234	A=0.52955	G=0.47045
African	Sub	4524	A=0.6543	G=0.3457
African Others	Sub	170	A=0.629	G=0.371
African American	Sub	4354	A=0.6553	G=0.3447
Asian	Sub	190	A=0.679	G=0.321
East Asian	Sub	148	A=0.635	G=0.365
Other Asian	Sub	42	A=0.83	G=0.17
Latin American 1	Sub	254	A=0.610	G=0.390
Latin American 2	Sub	1232	A=0.6380	G=0.3620
South Asian	Sub	4952	A=0.6525	G=0.3475
Other	Sub	4780	A=0.5475	G=0.4525

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	A=0.590234	G=0.409766
gnomAD - Genomes	Global	Study-wide	139998	A=0.571230	G=0.428770
gnomAD - Genomes	European	Sub	75824	A=0.51029	G=0.48971
gnomAD - Genomes	African	Sub	41944	A=0.65247	G=0.34753
gnomAD - Genomes	American	Sub	13640	A=0.63270	G=0.36730
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	A=0.6100	G=0.3900
gnomAD - Genomes	East Asian	Sub	3124	A=0.6341	G=0.3659
gnomAD - Genomes	Other	Sub	2148	A=0.5945	G=0.4055
Allele Frequency Aggregator	Total	Global	94166	A=0.54486	G=0.45514
Allele Frequency Aggregator	European	Sub	78234	A=0.52955	G=0.47045
Allele Frequency Aggregator	South Asian	Sub	4952	A=0.6525	G=0.3475
Allele Frequency Aggregator	Other	Sub	4780	A=0.5475	G=0.4525
Allele Frequency Aggregator	African	Sub	4524	A=0.6543	G=0.3457
Allele Frequency Aggregator	Latin American 2	Sub	1232	A=0.6380	G=0.3620
Allele Frequency Aggregator	Latin American 1	Sub	254	A=0.610	G=0.390
Allele Frequency Aggregator	Asian	Sub	190	A=0.679	G=0.321
14KJPN	JAPANESE	Study-wide	28256	A=0.64733	G=0.35267
8.3KJPN	JAPANESE	Study-wide	16760	A=0.64905	G=0.35095
1000Genomes_30x	Global	Study-wide	6404	A=0.6299	G=0.3701
1000Genomes_30x	African	Sub	1786	A=0.6691	G=0.3309
1000Genomes_30x	Europe	Sub	1266	A=0.5735	G=0.4265
1000Genomes_30x	South Asian	Sub	1202	A=0.6589	G=0.3411
1000Genomes_30x	East Asian	Sub	1170	A=0.6154	G=0.3846
1000Genomes_30x	American	Sub	980	A=0.613	G=0.387
1000Genomes	Global	Study-wide	5008	A=0.6308	G=0.3692
1000Genomes	African	Sub	1322	A=0.6725	G=0.3275
1000Genomes	East Asian	Sub	1008	A=0.6141	G=0.3859
1000Genomes	Europe	Sub	1006	A=0.5726	G=0.4274
1000Genomes	South Asian	Sub	978	A=0.664	G=0.336
1000Genomes	American	Sub	694	A=0.614	G=0.386
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.5263	G=0.4737
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.5086	G=0.4914
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.5049	G=0.4951
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.6256	G=0.3744
HGDP-CEPH-db Supplement 1	Global	Study-wide	2078	A=0.6328	G=0.3672
HGDP-CEPH-db Supplement 1	Est_Asia	Sub	466	A=0.612	G=0.388
HGDP-CEPH-db Supplement 1	Central_South_Asia	Sub	412	A=0.638	G=0.362
HGDP-CEPH-db Supplement 1	Middle_Est	Sub	350	A=0.646	G=0.354
HGDP-CEPH-db Supplement 1	Europe	Sub	320	A=0.606	G=0.394
HGDP-CEPH-db Supplement 1	Africa	Sub	242	A=0.669	G=0.331
HGDP-CEPH-db Supplement 1	America	Sub	216	A=0.662	G=0.338
HGDP-CEPH-db Supplement 1	Oceania	Sub	72	A=0.58	G=0.42
HapMap	Global	Study-wide	1890	A=0.6593	G=0.3407
HapMap	American	Sub	770	A=0.612	G=0.388
HapMap	African	Sub	692	A=0.723	G=0.277
HapMap	Asian	Sub	252	A=0.627	G=0.373
HapMap	Europe	Sub	176	A=0.665	G=0.335
Korean Genome Project	KOREAN	Study-wide	1832	A=0.6457	G=0.3543
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.526	G=0.474
Northern Sweden	ACPOP	Study-wide	600	A=0.465	G=0.535
SGDP_PRJ	Global	Study-wide	314	A=0.401	G=0.599
Qatari	Global	Study-wide	216	A=0.667	G=0.333
A Vietnamese Genetic Variation Database	Global	Study-wide	216	A=0.644	G=0.356
The Danish reference pan genome	Danish	Study-wide	40	A=0.57	G=0.42
Siberian	Global	Study-wide	36	A=0.42	G=0.58
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	6	A=0.3	G=0.7

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 2	NC_000002.12:g.168296426A>G
GRCh37.p13 chr 2	NC_000002.11:g.169152936A>G

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	A=	G
GRCh38.p14 chr 2	NC_000002.12:g.168296426=	NC_000002.12:g.168296426A>G
GRCh37.p13 chr 2	NC_000002.11:g.169152936=	NC_000002.11:g.169152936A>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#.

100 SubSNP, 22 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss2353807	Oct 23, 2000 (88)
2	WI_SSAHASNP	ss6427274	Feb 20, 2003 (111)
3	ABI	ss44180237	Mar 13, 2006 (126)
4	ILLUMINA	ss66770699	Dec 02, 2006 (127)
5	ILLUMINA	ss67122920	Dec 02, 2006 (127)
6	ILLUMINA	ss67461488	Dec 02, 2006 (127)
7	ILLUMINA	ss70439492	May 18, 2007 (127)
8	ILLUMINA	ss70627359	May 23, 2008 (130)
9	ILLUMINA	ss71176927	May 18, 2007 (127)
10	ILLUMINA	ss75790115	Dec 07, 2007 (129)
11	HGSV	ss77571965	Dec 07, 2007 (129)
12	HGSV	ss83610104	Dec 14, 2007 (130)
13	KRIBB_YJKIM	ss83812101	Dec 14, 2007 (130)
14	BCMHGSC_JDW	ss91431849	Mar 24, 2008 (129)
15	HUMANGENOME_JCVI	ss97097795	Feb 03, 2009 (130)
16	1000GENOMES	ss110227503	Jan 24, 2009 (130)
17	1000GENOMES	ss111238963	Jan 25, 2009 (130)
18	ILLUMINA-UK	ss117962143	Dec 01, 2009 (131)
19	ILLUMINA	ss121732452	Dec 01, 2009 (131)
20	ENSEMBL	ss132869368	Dec 01, 2009 (131)
21	ILLUMINA	ss153485926	Dec 01, 2009 (131)
22	GMI	ss157958671	Dec 01, 2009 (131)
23	ILLUMINA	ss159279452	Dec 01, 2009 (131)
24	COMPLETE_GENOMICS	ss164786118	Jul 04, 2010 (132)
25	COMPLETE_GENOMICS	ss167394787	Jul 04, 2010 (132)
26	ILLUMINA	ss170598191	Jul 04, 2010 (132)
27	ILLUMINA	ss172553689	Jul 04, 2010 (132)
28	BUSHMAN	ss201344197	Jul 04, 2010 (132)
29	1000GENOMES	ss219642391	Jul 14, 2010 (132)
30	1000GENOMES	ss231459749	Jul 14, 2010 (132)
31	1000GENOMES	ss238950199	Jul 15, 2010 (132)
32	BL	ss253661159	May 09, 2011 (134)
33	GMI	ss276778214	May 04, 2012 (137)
34	GMI	ss284481405	Apr 25, 2013 (138)
35	PJP	ss292420689	May 09, 2011 (134)
36	ILLUMINA	ss536885953	Sep 08, 2015 (146)
37	TISHKOFF	ss556022319	Apr 25, 2013 (138)
38	SSMP	ss649673570	Apr 25, 2013 (138)
39	ILLUMINA	ss825408476	Apr 01, 2015 (144)
40	ILLUMINA	ss832791597	Aug 21, 2014 (142)
41	ILLUMINA	ss833382427	Aug 21, 2014 (142)
42	EVA-GONL	ss977620674	Aug 21, 2014 (142)
43	JMKIDD_LAB	ss1069687993	Aug 21, 2014 (142)
44	1000GENOMES	ss1300340840	Aug 21, 2014 (142)
45	DDI	ss1428813965	Apr 01, 2015 (144)
46	EVA_GENOME_DK	ss1579188670	Apr 01, 2015 (144)
47	EVA_DECODE	ss1587058116	Apr 01, 2015 (144)
48	EVA_UK10K_ALSPAC	ss1605100453	Apr 01, 2015 (144)
49	EVA_UK10K_TWINSUK	ss1648094486	Apr 01, 2015 (144)
50	EVA_SVP	ss1712507660	Apr 01, 2015 (144)
51	HAMMER_LAB	ss1797881645	Sep 08, 2015 (146)
52	WEILL_CORNELL_DGM	ss1920872922	Feb 12, 2016 (147)
53	GENOMED	ss1968947554	Jul 19, 2016 (147)
54	JJLAB	ss2020970288	Sep 14, 2016 (149)
55	USC_VALOUEV	ss2149035123	Dec 20, 2016 (150)
56	HUMAN_LONGEVITY	ss2236398571	Dec 20, 2016 (150)
57	SYSTEMSBIOZJU	ss2624989264	Nov 08, 2017 (151)
58	GRF	ss2703672234	Nov 08, 2017 (151)
59	GNOMAD	ss2782570603	Nov 08, 2017 (151)
60	SWEGEN	ss2990828489	Nov 08, 2017 (151)
61	BIOINF_KMB_FNS_UNIBA	ss3024245566	Nov 08, 2017 (151)
62	CSHL	ss3344594884	Nov 08, 2017 (151)
63	ILLUMINA	ss3628216463	Oct 11, 2018 (152)
64	ILLUMINA	ss3638300596	Oct 11, 2018 (152)
65	ILLUMINA	ss3639154326	Oct 11, 2018 (152)
66	ILLUMINA	ss3639590093	Oct 11, 2018 (152)
67	ILLUMINA	ss3643266650	Oct 11, 2018 (152)
68	URBANLAB	ss3647201089	Oct 11, 2018 (152)
69	EGCUT_WGS	ss3658698466	Jul 13, 2019 (153)
70	EVA_DECODE	ss3705379614	Jul 13, 2019 (153)
71	ACPOP	ss3729086436	Jul 13, 2019 (153)
72	ILLUMINA	ss3744482728	Jul 13, 2019 (153)
73	EVA	ss3757693462	Jul 13, 2019 (153)
74	PACBIO	ss3784060627	Jul 13, 2019 (153)
75	PACBIO	ss3789613540	Jul 13, 2019 (153)
76	PACBIO	ss3794486537	Jul 13, 2019 (153)
77	KHV_HUMAN_GENOMES	ss3802051996	Jul 13, 2019 (153)
78	EVA	ss3827342113	Apr 25, 2020 (154)
79	EVA	ss3837088918	Apr 25, 2020 (154)
80	EVA	ss3842508705	Apr 25, 2020 (154)
81	HGDP	ss3847640834	Apr 25, 2020 (154)
82	SGDP_PRJ	ss3853928508	Apr 25, 2020 (154)
83	KRGDB	ss3899556988	Apr 25, 2020 (154)
84	KOGIC	ss3949456732	Apr 25, 2020 (154)
85	EVA	ss3984935882	Apr 26, 2021 (155)
86	EVA	ss4017032962	Apr 26, 2021 (155)
87	TOPMED	ss4532992972	Apr 26, 2021 (155)
88	TOMMO_GENOMICS	ss5155017942	Apr 26, 2021 (155)
89	1000G_HIGH_COVERAGE	ss5250892450	Oct 12, 2022 (156)
90	HUGCELL_USP	ss5450618112	Oct 12, 2022 (156)
91	EVA	ss5506681288	Oct 12, 2022 (156)
92	1000G_HIGH_COVERAGE	ss5527641993	Oct 12, 2022 (156)
93	SANFORD_IMAGENETICS	ss5630312373	Oct 12, 2022 (156)
94	TOMMO_GENOMICS	ss5685472355	Oct 12, 2022 (156)
95	YY_MCH	ss5802945300	Oct 12, 2022 (156)
96	EVA	ss5821147069	Oct 12, 2022 (156)
97	EVA	ss5852821391	Oct 12, 2022 (156)
98	EVA	ss5933391801	Oct 12, 2022 (156)
99	EVA	ss5956534834	Oct 12, 2022 (156)
100	EVA	ss5980094148	Oct 12, 2022 (156)
101	1000Genomes	NC_000002.11 - 169152936	Oct 11, 2018 (152)
102	1000Genomes_30x	NC_000002.12 - 168296426	Oct 12, 2022 (156)
103	The Avon Longitudinal Study of Parents and Children	NC_000002.11 - 169152936	Oct 11, 2018 (152)
104	Genetic variation in the Estonian population	NC_000002.11 - 169152936	Oct 11, 2018 (152)
105	The Danish reference pan genome	NC_000002.11 - 169152936	Apr 25, 2020 (154)
106	gnomAD - Genomes	NC_000002.12 - 168296426	Apr 26, 2021 (155)
107	Genome of the Netherlands Release 5	NC_000002.11 - 169152936	Apr 25, 2020 (154)
108	HGDP-CEPH-db Supplement 1	NC_000002.10 - 168861182	Apr 25, 2020 (154)
109	HapMap	NC_000002.12 - 168296426	Apr 25, 2020 (154)
110	KOREAN population from KRGDB	NC_000002.11 - 169152936	Apr 25, 2020 (154)
111	Korean Genome Project	NC_000002.12 - 168296426	Apr 25, 2020 (154)
112	Northern Sweden	NC_000002.11 - 169152936	Jul 13, 2019 (153)
113	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000002.11 - 169152936	Apr 26, 2021 (155)
114	Qatari	NC_000002.11 - 169152936	Apr 25, 2020 (154)
115	SGDP_PRJ	NC_000002.11 - 169152936	Apr 25, 2020 (154)
116	Siberian	NC_000002.11 - 169152936	Apr 25, 2020 (154)
117	8.3KJPN	NC_000002.11 - 169152936	Apr 26, 2021 (155)
118	14KJPN	NC_000002.12 - 168296426	Oct 12, 2022 (156)
119	TopMed	NC_000002.12 - 168296426	Apr 26, 2021 (155)
120	UK 10K study - Twins	NC_000002.11 - 169152936	Oct 11, 2018 (152)
121	A Vietnamese Genetic Variation Database	NC_000002.11 - 169152936	Jul 13, 2019 (153)
122	ALFA	NC_000002.12 - 168296426	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)
rs56895955	May 23, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss77571965, ss83610104, ss3639154326, ss3639590093	NC_000002.9:168978442:A:G	NC_000002.12:168296425:A:G	(self)
318726, ss91431849, ss110227503, ss111238963, ss117962143, ss164786118, ss167394787, ss201344197, ss253661159, ss276778214, ss284481405, ss292420689, ss825408476, ss1587058116, ss1712507660, ss3643266650, ss3847640834	NC_000002.10:168861181:A:G	NC_000002.12:168296425:A:G	(self)
11394849, 6286444, 4436714, 5353609, 2761674, 6734382, 2371301, 161809, 2914852, 5945488, 1551477, 12987249, 6286444, 1366044, ss219642391, ss231459749, ss238950199, ss536885953, ss556022319, ss649673570, ss832791597, ss833382427, ss977620674, ss1069687993, ss1300340840, ss1428813965, ss1579188670, ss1605100453, ss1648094486, ss1797881645, ss1920872922, ss1968947554, ss2020970288, ss2149035123, ss2624989264, ss2703672234, ss2782570603, ss2990828489, ss3344594884, ss3628216463, ss3638300596, ss3658698466, ss3729086436, ss3744482728, ss3757693462, ss3784060627, ss3789613540, ss3794486537, ss3827342113, ss3837088918, ss3853928508, ss3899556988, ss3984935882, ss4017032962, ss5155017942, ss5506681288, ss5630312373, ss5821147069, ss5956534834, ss5980094148	NC_000002.11:169152935:A:G	NC_000002.12:168296425:A:G	(self)
15167928, 81237761, 1944362, 5834733, 19309459, 336815851, 5577039752, ss2236398571, ss3024245566, ss3647201089, ss3705379614, ss3802051996, ss3842508705, ss3949456732, ss4532992972, ss5250892450, ss5450618112, ss5527641993, ss5685472355, ss5802945300, ss5852821391, ss5933391801	NC_000002.12:168296425:A:G	NC_000002.12:168296425:A:G	(self)
ss2353807, ss6427274, ss44180237, ss66770699, ss67122920, ss67461488, ss70439492, ss70627359, ss71176927, ss75790115, ss83812101, ss97097795, ss121732452, ss132869368, ss153485926, ss157958671, ss159279452, ss170598191, ss172553689	NT_005403.17:19362353:A:G	NC_000002.12:168296425:A: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 rs1517336

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

rs1517336