Name: rs2815342
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.

rs2815342

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:67066630 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.136424 (36110/264690, TOPMED)
G=0.147789 (20705/140098, GnomAD)
G=0.01776 (502/28258, 14KJPN) (+ 17 more)
G=0.14336 (2708/18890, ALFA)
G=0.01677 (281/16760, 8.3KJPN)
G=0.1054 (675/6404, 1000G_30x)
G=0.1042 (522/5008, 1000G)
G=0.1520 (681/4480, Estonian)
G=0.1279 (493/3854, ALSPAC)
G=0.1270 (471/3708, TWINSUK)
G=0.0092 (27/2930, KOREAN)
G=0.0076 (14/1832, Korea1K)
G=0.127 (127/998, GoNL)
G=0.172 (103/600, NorthernSweden)
G=0.067 (37/552, SGDP_PRJ)
G=0.199 (43/216, Qatari)
G=0.051 (11/214, Vietnamese)
G=0.079 (16/202, HapMap)
G=0.04 (2/56, Siberian)
G=0.07 (3/40, GENOME_DK)

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	18890	G=0.14336	A=0.85664
European	Sub	14286	G=0.14252	A=0.85748
African	Sub	2946	G=0.1697	A=0.8303
African Others	Sub	114	G=0.184	A=0.816
African American	Sub	2832	G=0.1691	A=0.8309
Asian	Sub	112	G=0.027	A=0.973
East Asian	Sub	86	G=0.02	A=0.98
Other Asian	Sub	26	G=0.04	A=0.96
Latin American 1	Sub	146	G=0.144	A=0.856
Latin American 2	Sub	610	G=0.082	A=0.918
South Asian	Sub	98	G=0.01	A=0.99
Other	Sub	692	G=0.140	A=0.860

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=0.136424	A=0.863576
gnomAD - Genomes	Global	Study-wide	140098	G=0.147789	A=0.852211
gnomAD - Genomes	European	Sub	75884	G=0.14939	A=0.85061
gnomAD - Genomes	African	Sub	41958	G=0.17015	A=0.82985
gnomAD - Genomes	American	Sub	13654	G=0.10349	A=0.89651
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	G=0.1276	A=0.8724
gnomAD - Genomes	East Asian	Sub	3130	G=0.0275	A=0.9725
gnomAD - Genomes	Other	Sub	2148	G=0.1429	A=0.8571
14KJPN	JAPANESE	Study-wide	28258	G=0.01776	A=0.98224
Allele Frequency Aggregator	Total	Global	18890	G=0.14336	A=0.85664
Allele Frequency Aggregator	European	Sub	14286	G=0.14252	A=0.85748
Allele Frequency Aggregator	African	Sub	2946	G=0.1697	A=0.8303
Allele Frequency Aggregator	Other	Sub	692	G=0.140	A=0.860
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.082	A=0.918
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.144	A=0.856
Allele Frequency Aggregator	Asian	Sub	112	G=0.027	A=0.973
Allele Frequency Aggregator	South Asian	Sub	98	G=0.01	A=0.99
8.3KJPN	JAPANESE	Study-wide	16760	G=0.01677	A=0.98323
1000Genomes_30x	Global	Study-wide	6404	G=0.1054	A=0.8946
1000Genomes_30x	African	Sub	1786	G=0.1697	A=0.8303
1000Genomes_30x	Europe	Sub	1266	G=0.1793	A=0.8207
1000Genomes_30x	South Asian	Sub	1202	G=0.0175	A=0.9825
1000Genomes_30x	East Asian	Sub	1170	G=0.0308	A=0.9692
1000Genomes_30x	American	Sub	980	G=0.090	A=0.910
1000Genomes	Global	Study-wide	5008	G=0.1042	A=0.8958
1000Genomes	African	Sub	1322	G=0.1687	A=0.8313
1000Genomes	East Asian	Sub	1008	G=0.0278	A=0.9722
1000Genomes	Europe	Sub	1006	G=0.1879	A=0.8121
1000Genomes	South Asian	Sub	978	G=0.018	A=0.982
1000Genomes	American	Sub	694	G=0.092	A=0.908
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.1520	A=0.8480
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.1279	A=0.8721
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.1270	A=0.8730
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.0092	A=0.9908, T=0.0000
Korean Genome Project	KOREAN	Study-wide	1832	G=0.0076	A=0.9924
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.127	A=0.873
Northern Sweden	ACPOP	Study-wide	600	G=0.172	A=0.828
SGDP_PRJ	Global	Study-wide	552	G=0.067	A=0.933
Qatari	Global	Study-wide	216	G=0.199	A=0.801
A Vietnamese Genetic Variation Database	Global	Study-wide	214	G=0.051	A=0.949
HapMap	Global	Study-wide	202	G=0.079	A=0.921
HapMap	African	Sub	118	G=0.127	A=0.873
HapMap	Asian	Sub	84	G=0.01	A=0.99
Siberian	Global	Study-wide	56	G=0.04	A=0.96
The Danish reference pan genome	Danish	Study-wide	40	G=0.07	A=0.93

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 1	NC_000001.11:g.67066630G>A
GRCh38.p14 chr 1	NC_000001.11:g.67066630G>T
GRCh37.p13 chr 1	NC_000001.10:g.67532313G>A
GRCh37.p13 chr 1	NC_000001.10:g.67532313G>T

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	T
GRCh38.p14 chr 1	NC_000001.11:g.67066630=	NC_000001.11:g.67066630G>A	NC_000001.11:g.67066630G>T
GRCh37.p13 chr 1	NC_000001.10:g.67532313=	NC_000001.10:g.67532313G>A	NC_000001.10:g.67532313G>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#.

82 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss3987744	Sep 28, 2001 (100)
2	TSC-CSHL	ss4051626	Nov 05, 2001 (101)
3	BCM_SSAHASNP	ss9832747	Jul 11, 2003 (116)
4	WI_SSAHASNP	ss11363968	Jul 11, 2003 (116)
5	SC_SNP	ss13035793	Dec 05, 2003 (120)
6	CSHL-HAPMAP	ss19147787	Feb 27, 2004 (120)
7	SSAHASNP	ss20528193	Apr 05, 2004 (121)
8	ABI	ss41161269	Mar 15, 2006 (126)
9	HGSV	ss78301073	Dec 07, 2007 (129)
10	HGSV	ss83337401	Dec 15, 2007 (130)
11	BCMHGSC_JDW	ss87509376	Mar 23, 2008 (129)
12	HUMANGENOME_JCVI	ss99214969	Feb 06, 2009 (130)
13	BGI	ss106572916	Feb 06, 2009 (130)
14	1000GENOMES	ss108275900	Jan 23, 2009 (130)
15	1000GENOMES	ss110579570	Jan 25, 2009 (130)
16	ILLUMINA-UK	ss118768845	Dec 01, 2009 (131)
17	ENSEMBL	ss137985470	Dec 01, 2009 (131)
18	ENSEMBL	ss138914005	Dec 01, 2009 (131)
19	GMI	ss155121760	Dec 01, 2009 (131)
20	COMPLETE_GENOMICS	ss163474369	Jul 04, 2010 (132)
21	COMPLETE_GENOMICS	ss164469733	Jul 04, 2010 (132)
22	COMPLETE_GENOMICS	ss166648719	Jul 04, 2010 (132)
23	BUSHMAN	ss198567900	Jul 04, 2010 (132)
24	BCM-HGSC-SUB	ss205374346	Jul 04, 2010 (132)
25	1000GENOMES	ss218431574	Jul 14, 2010 (132)
26	1000GENOMES	ss230568825	Jul 14, 2010 (132)
27	1000GENOMES	ss238256778	Jul 15, 2010 (132)
28	BL	ss253154965	May 09, 2011 (134)
29	GMI	ss275860065	May 04, 2012 (137)
30	GMI	ss284065110	Apr 25, 2013 (138)
31	PJP	ss290528978	May 09, 2011 (134)
32	TISHKOFF	ss554207794	Apr 25, 2013 (138)
33	SSMP	ss648082001	Apr 25, 2013 (138)
34	EVA-GONL	ss975248190	Aug 21, 2014 (142)
35	JMKIDD_LAB	ss1067954775	Aug 21, 2014 (142)
36	1000GENOMES	ss1291226931	Aug 21, 2014 (142)
37	DDI	ss1425837846	Apr 01, 2015 (144)
38	EVA_GENOME_DK	ss1574121257	Apr 01, 2015 (144)
39	EVA_DECODE	ss1584617708	Apr 01, 2015 (144)
40	EVA_UK10K_ALSPAC	ss1600352123	Apr 01, 2015 (144)
41	EVA_UK10K_TWINSUK	ss1643346156	Apr 01, 2015 (144)
42	HAMMER_LAB	ss1794497698	Sep 08, 2015 (146)
43	WEILL_CORNELL_DGM	ss1918456104	Feb 12, 2016 (147)
44	GENOMED	ss1966766826	Jul 19, 2016 (147)
45	JJLAB	ss2019745470	Sep 14, 2016 (149)
46	USC_VALOUEV	ss2147761280	Dec 20, 2016 (150)
47	HUMAN_LONGEVITY	ss2163201679	Dec 20, 2016 (150)
48	SYSTEMSBIOZJU	ss2624386373	Nov 08, 2017 (151)
49	GRF	ss2697678916	Nov 08, 2017 (151)
50	GNOMAD	ss2756091623	Nov 08, 2017 (151)
51	SWEGEN	ss2986950824	Nov 08, 2017 (151)
52	BIOINF_KMB_FNS_UNIBA	ss3023634479	Nov 08, 2017 (151)
53	CSHL	ss3343493490	Nov 08, 2017 (151)
54	URBANLAB	ss3646681553	Oct 11, 2018 (152)
55	EGCUT_WGS	ss3655020975	Jul 12, 2019 (153)
56	EVA_DECODE	ss3686936324	Jul 12, 2019 (153)
57	ACPOP	ss3727120687	Jul 12, 2019 (153)
58	EVA	ss3746308119	Jul 12, 2019 (153)
59	PACBIO	ss3783433288	Jul 12, 2019 (153)
60	PACBIO	ss3789087838	Jul 12, 2019 (153)
61	PACBIO	ss3793960618	Jul 12, 2019 (153)
62	KHV_HUMAN_GENOMES	ss3799314857	Jul 12, 2019 (153)
63	EVA	ss3826215349	Apr 25, 2020 (154)
64	EVA	ss3836495136	Apr 25, 2020 (154)
65	EVA	ss3841901686	Apr 25, 2020 (154)
66	SGDP_PRJ	ss3849022184	Apr 25, 2020 (154)
67	KRGDB	ss3894050194	Apr 25, 2020 (154)
68	KOGIC	ss3944675994	Apr 25, 2020 (154)
69	TOPMED	ss4452688349	Apr 25, 2021 (155)
70	TOMMO_GENOMICS	ss5144324856	Apr 25, 2021 (155)
71	1000G_HIGH_COVERAGE	ss5242559402	Oct 12, 2022 (156)
72	EVA	ss5319261917	Oct 12, 2022 (156)
73	HUGCELL_USP	ss5443593744	Oct 12, 2022 (156)
74	EVA	ss5505880436	Oct 12, 2022 (156)
75	1000G_HIGH_COVERAGE	ss5514981999	Oct 12, 2022 (156)
76	SANFORD_IMAGENETICS	ss5625695611	Oct 12, 2022 (156)
77	TOMMO_GENOMICS	ss5669204246	Oct 12, 2022 (156)
78	YY_MCH	ss5800669487	Oct 12, 2022 (156)
79	EVA	ss5832072496	Oct 12, 2022 (156)
80	EVA	ss5848942279	Oct 12, 2022 (156)
81	EVA	ss5908596125	Oct 12, 2022 (156)
82	EVA	ss5937534157	Oct 12, 2022 (156)
83	1000Genomes	NC_000001.10 - 67532313	Oct 11, 2018 (152)
84	1000Genomes_30x	NC_000001.11 - 67066630	Oct 12, 2022 (156)
85	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 67532313	Oct 11, 2018 (152)
86	Genetic variation in the Estonian population	NC_000001.10 - 67532313	Oct 11, 2018 (152)
87	The Danish reference pan genome	NC_000001.10 - 67532313	Apr 25, 2020 (154)
88	gnomAD - Genomes	NC_000001.11 - 67066630	Apr 25, 2021 (155)
89	Genome of the Netherlands Release 5	NC_000001.10 - 67532313	Apr 25, 2020 (154)
90	HapMap	NC_000001.11 - 67066630	Apr 25, 2020 (154)
91	KOREAN population from KRGDB	NC_000001.10 - 67532313	Apr 25, 2020 (154)
92	Korean Genome Project	NC_000001.11 - 67066630	Apr 25, 2020 (154)
93	Northern Sweden	NC_000001.10 - 67532313	Jul 12, 2019 (153)
94	Qatari	NC_000001.10 - 67532313	Apr 25, 2020 (154)
95	SGDP_PRJ	NC_000001.10 - 67532313	Apr 25, 2020 (154)
96	Siberian	NC_000001.10 - 67532313	Apr 25, 2020 (154)
97	8.3KJPN	NC_000001.10 - 67532313	Apr 25, 2021 (155)
98	14KJPN	NC_000001.11 - 67066630	Oct 12, 2022 (156)
99	TopMed	NC_000001.11 - 67066630	Apr 25, 2021 (155)
100	UK 10K study - Twins	NC_000001.10 - 67532313	Oct 11, 2018 (152)
101	A Vietnamese Genetic Variation Database	NC_000001.10 - 67532313	Jul 12, 2019 (153)
102	ALFA	NC_000001.11 - 67066630	Apr 25, 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)
rs9436348	Feb 27, 2004 (120)
rs60357071	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss78301073, ss83337401	NC_000001.8:67244333:G:A	NC_000001.11:67066629:G:A	(self)
ss87509376, ss108275900, ss110579570, ss118768845, ss163474369, ss164469733, ss166648719, ss198567900, ss205374346, ss253154965, ss275860065, ss284065110, ss290528978, ss1584617708	NC_000001.9:67304900:G:A	NC_000001.11:67066629:G:A	(self)
1957285, 1072257, 759223, 1536696, 457637, 1227588, 405552, 498034, 1039164, 277634, 2294163, 1072257, 224654, ss218431574, ss230568825, ss238256778, ss554207794, ss648082001, ss975248190, ss1067954775, ss1291226931, ss1425837846, ss1574121257, ss1600352123, ss1643346156, ss1794497698, ss1918456104, ss1966766826, ss2019745470, ss2147761280, ss2624386373, ss2697678916, ss2756091623, ss2986950824, ss3343493490, ss3655020975, ss3727120687, ss3746308119, ss3783433288, ss3789087838, ss3793960618, ss3826215349, ss3836495136, ss3849022184, ss3894050194, ss5144324856, ss5319261917, ss5505880436, ss5625695611, ss5832072496, ss5937534157	NC_000001.10:67532312:G:A	NC_000001.11:67066629:G:A	(self)
2507934, 13804927, 88106, 1053995, 3041350, 16294684, 3415414629, ss2163201679, ss3023634479, ss3646681553, ss3686936324, ss3799314857, ss3841901686, ss3944675994, ss4452688349, ss5242559402, ss5443593744, ss5514981999, ss5669204246, ss5800669487, ss5848942279, ss5908596125	NC_000001.11:67066629:G:A	NC_000001.11:67066629:G:A	(self)
ss9832747, ss11363968, ss13035793	NT_032977.5:19981222:G:A	NC_000001.11:67066629:G:A	(self)
ss19147787, ss20528193	NT_032977.6:29095381:G:A	NC_000001.11:67066629:G:A	(self)
ss3987744, ss4051626, ss41161269, ss99214969, ss106572916, ss137985470, ss138914005, ss155121760	NT_032977.9:37504230:G:A	NC_000001.11:67066629:G:A	(self)
1227588, ss3894050194	NC_000001.10:67532312:G:T	NC_000001.11:67066629: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 rs2815342

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

rs2815342