Name: rs2662809
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.

rs2662809

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr12:127223045 (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>C / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.322075 (85250/264690, TOPMED)
G=0.332194 (46444/139810, GnomAD)
G=0.16565 (4681/28258, 14KJPN) (+ 12 more)
G=0.16360 (2742/16760, 8.3KJPN)
G=0.4789 (3880/8102, ALFA)
G=0.2644 (1693/6404, 1000G_30x)
G=0.2610 (1307/5008, 1000G)
G=0.1652 (484/2930, KOREAN)
G=0.452 (451/998, GoNL)
G=0.362 (217/600, NorthernSweden)
G=0.172 (90/522, SGDP_PRJ)
G=0.259 (56/216, Qatari)
G=0.137 (29/212, Vietnamese)
G=0.17 (9/52, Siberian)
G=0.17 (7/40, 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	8102	G=0.4789	C=0.5211, T=0.0000
European	Sub	7568	G=0.4527	C=0.5473, T=0.0000
African	Sub	398	G=0.854	C=0.146, T=0.000
African Others	Sub	14	G=0.79	C=0.21, T=0.00
African American	Sub	384	G=0.857	C=0.143, T=0.000
Asian	Sub	8	G=0.8	C=0.2, T=0.0
East Asian	Sub	6	G=0.7	C=0.3, T=0.0
Other Asian	Sub	2	G=1.0	C=0.0, T=0.0
Latin American 1	Sub	16	G=1.00	C=0.00, T=0.00
Latin American 2	Sub	26	G=1.00	C=0.00, T=0.00
South Asian	Sub	8	G=0.9	C=0.1, T=0.0
Other	Sub	78	G=0.76	C=0.24, T=0.00

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=0.322075	C=0.677925
gnomAD - Genomes	Global	Study-wide	139810	G=0.332194	C=0.667806
gnomAD - Genomes	European	Sub	75736	G=0.35515	C=0.64485
gnomAD - Genomes	African	Sub	41866	G=0.32425	C=0.67575
gnomAD - Genomes	American	Sub	13628	G=0.27099	C=0.72901
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	G=0.3494	C=0.6506
gnomAD - Genomes	East Asian	Sub	3110	G=0.1379	C=0.8621
gnomAD - Genomes	Other	Sub	2150	G=0.3205	C=0.6795
14KJPN	JAPANESE	Study-wide	28258	G=0.16565	C=0.83435
8.3KJPN	JAPANESE	Study-wide	16760	G=0.16360	C=0.83640
Allele Frequency Aggregator	Total	Global	8102	G=0.4789	C=0.5211, T=0.0000
Allele Frequency Aggregator	European	Sub	7568	G=0.4527	C=0.5473, T=0.0000
Allele Frequency Aggregator	African	Sub	398	G=0.854	C=0.146, T=0.000
Allele Frequency Aggregator	Other	Sub	78	G=0.76	C=0.24, T=0.00
Allele Frequency Aggregator	Latin American 2	Sub	26	G=1.00	C=0.00, T=0.00
Allele Frequency Aggregator	Latin American 1	Sub	16	G=1.00	C=0.00, T=0.00
Allele Frequency Aggregator	South Asian	Sub	8	G=0.9	C=0.1, T=0.0
Allele Frequency Aggregator	Asian	Sub	8	G=0.8	C=0.2, T=0.0
1000Genomes_30x	Global	Study-wide	6404	G=0.2644	C=0.7356
1000Genomes_30x	African	Sub	1786	G=0.3287	C=0.6713
1000Genomes_30x	Europe	Sub	1266	G=0.3310	C=0.6690
1000Genomes_30x	South Asian	Sub	1202	G=0.2779	C=0.7221
1000Genomes_30x	East Asian	Sub	1170	G=0.1342	C=0.8658
1000Genomes_30x	American	Sub	980	G=0.200	C=0.800
1000Genomes	Global	Study-wide	5008	G=0.2610	C=0.7390
1000Genomes	African	Sub	1322	G=0.3230	C=0.6770
1000Genomes	East Asian	Sub	1008	G=0.1369	C=0.8631
1000Genomes	Europe	Sub	1006	G=0.3250	C=0.6750
1000Genomes	South Asian	Sub	978	G=0.281	C=0.719
1000Genomes	American	Sub	694	G=0.202	C=0.798
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.1652	C=0.8348, T=0.0000
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.452	C=0.548
Northern Sweden	ACPOP	Study-wide	600	G=0.362	C=0.638
SGDP_PRJ	Global	Study-wide	522	G=0.172	C=0.828
Qatari	Global	Study-wide	216	G=0.259	C=0.741
A Vietnamese Genetic Variation Database	Global	Study-wide	212	G=0.137	C=0.863
Siberian	Global	Study-wide	52	G=0.17	C=0.83
The Danish reference pan genome	Danish	Study-wide	40	G=0.17	C=0.82

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 12	NC_000012.12:g.127223045G>C
GRCh38.p14 chr 12	NC_000012.12:g.127223045G>T
GRCh37.p13 chr 12	NC_000012.11:g.127707590G>C
GRCh37.p13 chr 12	NC_000012.11:g.127707590G>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=	C	T
GRCh38.p14 chr 12	NC_000012.12:g.127223045=	NC_000012.12:g.127223045G>C	NC_000012.12:g.127223045G>T
GRCh37.p13 chr 12	NC_000012.11:g.127707590=	NC_000012.11:g.127707590G>C	NC_000012.11:g.127707590G>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, 15 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss1339968	Oct 08, 2002 (108)
2	SC_JCM	ss3756167	Sep 28, 2001 (100)
3	TSC-CSHL	ss5170527	Oct 08, 2002 (108)
4	TSC-CSHL	ss5387895	Oct 08, 2002 (108)
5	SC_JCM	ss5770295	Feb 20, 2003 (111)
6	WI_SSAHASNP	ss6573363	Feb 20, 2003 (111)
7	SC_SNP	ss15822914	Feb 27, 2004 (120)
8	CSHL-HAPMAP	ss17459918	Feb 27, 2004 (120)
9	SSAHASNP	ss20912551	Apr 05, 2004 (121)
10	HGSV	ss81021490	Dec 15, 2007 (130)
11	HGSV	ss81466110	Dec 15, 2007 (130)
12	HUMANGENOME_JCVI	ss97349631	Feb 06, 2009 (130)
13	BGI	ss105135639	Feb 06, 2009 (130)
14	1000GENOMES	ss112524443	Jan 25, 2009 (130)
15	ILLUMINA-UK	ss119775265	Dec 01, 2009 (131)
16	ENSEMBL	ss137546830	Dec 01, 2009 (131)
17	GMI	ss158026203	Dec 01, 2009 (131)
18	BUSHMAN	ss198835440	Jul 04, 2010 (132)
19	BCM-HGSC-SUB	ss208313987	Jul 04, 2010 (132)
20	1000GENOMES	ss211357178	Jul 14, 2010 (132)
21	1000GENOMES	ss226022806	Jul 14, 2010 (132)
22	1000GENOMES	ss236132114	Jul 15, 2010 (132)
23	1000GENOMES	ss242651722	Jul 15, 2010 (132)
24	BL	ss255383610	May 09, 2011 (134)
25	GMI	ss281591432	May 04, 2012 (137)
26	GMI	ss286645722	Apr 25, 2013 (138)
27	PJP	ss291363935	May 09, 2011 (134)
28	TISHKOFF	ss563482023	Apr 25, 2013 (138)
29	SSMP	ss659066801	Apr 25, 2013 (138)
30	EVA-GONL	ss990082355	Aug 21, 2014 (142)
31	1000GENOMES	ss1347108015	Aug 21, 2014 (142)
32	DDI	ss1427089605	Apr 01, 2015 (144)
33	EVA_GENOME_DK	ss1576597028	Apr 01, 2015 (144)
34	HAMMER_LAB	ss1807474253	Sep 08, 2015 (146)
35	WEILL_CORNELL_DGM	ss1933439198	Feb 12, 2016 (147)
36	JJLAB	ss2027475238	Sep 14, 2016 (149)
37	USC_VALOUEV	ss2155833112	Dec 20, 2016 (150)
38	HUMAN_LONGEVITY	ss2194161946	Dec 20, 2016 (150)
39	GRF	ss2700194435	Nov 08, 2017 (151)
40	GNOMAD	ss2916508482	Nov 08, 2017 (151)
41	SWEGEN	ss3010543502	Nov 08, 2017 (151)
42	CSHL	ss3350304873	Nov 08, 2017 (151)
43	URBANLAB	ss3649946609	Oct 12, 2018 (152)
44	EVA_DECODE	ss3694709771	Jul 13, 2019 (153)
45	ACPOP	ss3739485819	Jul 13, 2019 (153)
46	EVA	ss3751110636	Jul 13, 2019 (153)
47	KHV_HUMAN_GENOMES	ss3816437664	Jul 13, 2019 (153)
48	EVA	ss3833388345	Apr 27, 2020 (154)
49	EVA	ss3840264873	Apr 27, 2020 (154)
50	EVA	ss3845754122	Apr 27, 2020 (154)
51	SGDP_PRJ	ss3879359777	Apr 27, 2020 (154)
52	KRGDB	ss3928146874	Apr 27, 2020 (154)
53	TOPMED	ss4936752078	Apr 26, 2021 (155)
54	TOMMO_GENOMICS	ss5208718525	Apr 26, 2021 (155)
55	1000G_HIGH_COVERAGE	ss5292655195	Oct 16, 2022 (156)
56	EVA	ss5408987395	Oct 16, 2022 (156)
57	HUGCELL_USP	ss5487214814	Oct 16, 2022 (156)
58	EVA	ss5510879893	Oct 16, 2022 (156)
59	1000G_HIGH_COVERAGE	ss5591073817	Oct 16, 2022 (156)
60	SANFORD_IMAGENETICS	ss5654190705	Oct 16, 2022 (156)
61	TOMMO_GENOMICS	ss5759216357	Oct 16, 2022 (156)
62	YY_MCH	ss5813749102	Oct 16, 2022 (156)
63	EVA	ss5838678614	Oct 16, 2022 (156)
64	EVA	ss5850599324	Oct 16, 2022 (156)
65	EVA	ss5906498995	Oct 16, 2022 (156)
66	EVA	ss5945605389	Oct 16, 2022 (156)
67	1000Genomes	NC_000012.11 - 127707590	Oct 12, 2018 (152)
68	1000Genomes_30x	NC_000012.12 - 127223045	Oct 16, 2022 (156)
69	The Danish reference pan genome	NC_000012.11 - 127707590	Apr 27, 2020 (154)
70	gnomAD - Genomes	NC_000012.12 - 127223045	Apr 26, 2021 (155)
71	Genome of the Netherlands Release 5	NC_000012.11 - 127707590	Apr 27, 2020 (154)
72	KOREAN population from KRGDB	NC_000012.11 - 127707590	Apr 27, 2020 (154)
73	Northern Sweden	NC_000012.11 - 127707590	Jul 13, 2019 (153)
74	Qatari	NC_000012.11 - 127707590	Apr 27, 2020 (154)
75	SGDP_PRJ	NC_000012.11 - 127707590	Apr 27, 2020 (154)
76	Siberian	NC_000012.11 - 127707590	Apr 27, 2020 (154)
77	8.3KJPN	NC_000012.11 - 127707590	Apr 26, 2021 (155)
78	14KJPN	NC_000012.12 - 127223045	Oct 16, 2022 (156)
79	TopMed	NC_000012.12 - 127223045	Apr 26, 2021 (155)
80	A Vietnamese Genetic Variation Database	NC_000012.11 - 127707590	Jul 13, 2019 (153)
81	ALFA	NC_000012.12 - 127223045	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)
rs60073970	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss81021490, ss81466110	NC_000012.9:126232469:G:C	NC_000012.12:127223044:G:C	(self)
ss112524443, ss119775265, ss198835440, ss208313987, ss211357178, ss255383610, ss281591432, ss286645722, ss291363935	NC_000012.10:126273542:G:C	NC_000012.12:127223044:G:C	(self)
59936500, 3174040, 14846052, 35324268, 12770684, 15481128, 31376757, 8349466, 66687832, 7382651, ss226022806, ss236132114, ss242651722, ss563482023, ss659066801, ss990082355, ss1347108015, ss1427089605, ss1576597028, ss1807474253, ss1933439198, ss2027475238, ss2155833112, ss2700194435, ss2916508482, ss3010543502, ss3350304873, ss3739485819, ss3751110636, ss3833388345, ss3840264873, ss3879359777, ss3928146874, ss5208718525, ss5408987395, ss5510879893, ss5654190705, ss5838678614, ss5945605389	NC_000012.11:127707589:G:C	NC_000012.12:127223044:G:C	(self)
78599752, 422732253, 93053461, 152297735, 1098105521, ss2194161946, ss3649946609, ss3694709771, ss3816437664, ss3845754122, ss4936752078, ss5292655195, ss5487214814, ss5591073817, ss5759216357, ss5813749102, ss5850599324, ss5906498995	NC_000012.12:127223044:G:C	NC_000012.12:127223044:G:C	(self)
ss15822914, ss17459918, ss20912551	NT_009755.16:5016742:G:C	NC_000012.12:127223044:G:C	(self)
ss1339968, ss3756167, ss5170527, ss5387895, ss5770295, ss6573363, ss97349631, ss105135639, ss137546830, ss158026203	NT_009755.19:5126966:G:C	NC_000012.12:127223044:G:C	(self)
35324268, ss3928146874	NC_000012.11:127707589:G:T	NC_000012.12:127223044:G:T	(self)
1098105521, ss2194161946	NC_000012.12:127223044:G:T	NC_000012.12:127223044: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 rs2662809

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

rs2662809