Name: rs2201961
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.

rs2201961

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr15:87278722 (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: A=0.223631 (59193/264690, TOPMED)
A=0.217458 (30361/139618, GnomAD)
A=0.23268 (6575/28258, 14KJPN) (+ 16 more)
A=0.23669 (4471/18890, ALFA)
A=0.23234 (3894/16760, 8.3KJPN)
A=0.2477 (1586/6404, 1000G_30x)
A=0.2484 (1244/5008, 1000G)
A=0.2344 (1050/4480, Estonian)
A=0.2486 (958/3854, ALSPAC)
A=0.2570 (953/3708, TWINSUK)
A=0.2222 (651/2930, KOREAN)
A=0.270 (269/998, GoNL)
A=0.245 (147/600, NorthernSweden)
T=0.372 (113/304, SGDP_PRJ)
A=0.380 (82/216, Qatari)
A=0.276 (59/214, Vietnamese)
A=0.30 (12/40, GENOME_DK)
T=0.5 (5/10, Siberian)
A=0.5 (5/10, Siberian)

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	T=0.76331	A=0.23669
European	Sub	14286	T=0.74899	A=0.25101
African	Sub	2946	T=0.8618	A=0.1382
African Others	Sub	114	T=0.886	A=0.114
African American	Sub	2832	T=0.8609	A=0.1391
Asian	Sub	112	T=0.670	A=0.330
East Asian	Sub	86	T=0.66	A=0.34
Other Asian	Sub	26	T=0.69	A=0.31
Latin American 1	Sub	146	T=0.733	A=0.267
Latin American 2	Sub	610	T=0.703	A=0.297
South Asian	Sub	98	T=0.59	A=0.41
Other	Sub	692	T=0.738	A=0.262

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=0.776369	A=0.223631
gnomAD - Genomes	Global	Study-wide	139618	T=0.782542	A=0.217458
gnomAD - Genomes	European	Sub	75784	T=0.75323	A=0.24677
gnomAD - Genomes	African	Sub	41658	T=0.86980	A=0.13020
gnomAD - Genomes	American	Sub	13600	T=0.75029	A=0.24971
gnomAD - Genomes	Ashkenazi Jewish	Sub	3316	T=0.5464	A=0.4536
gnomAD - Genomes	East Asian	Sub	3122	T=0.7396	A=0.2604
gnomAD - Genomes	Other	Sub	2138	T=0.7554	A=0.2446
14KJPN	JAPANESE	Study-wide	28258	T=0.76732	A=0.23268
Allele Frequency Aggregator	Total	Global	18890	T=0.76331	A=0.23669
Allele Frequency Aggregator	European	Sub	14286	T=0.74899	A=0.25101
Allele Frequency Aggregator	African	Sub	2946	T=0.8618	A=0.1382
Allele Frequency Aggregator	Other	Sub	692	T=0.738	A=0.262
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.703	A=0.297
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.733	A=0.267
Allele Frequency Aggregator	Asian	Sub	112	T=0.670	A=0.330
Allele Frequency Aggregator	South Asian	Sub	98	T=0.59	A=0.41
8.3KJPN	JAPANESE	Study-wide	16760	T=0.76766	A=0.23234
1000Genomes_30x	Global	Study-wide	6404	T=0.7523	A=0.2477
1000Genomes_30x	African	Sub	1786	T=0.8880	A=0.1120
1000Genomes_30x	Europe	Sub	1266	T=0.7512	A=0.2488
1000Genomes_30x	South Asian	Sub	1202	T=0.5408	A=0.4592
1000Genomes_30x	East Asian	Sub	1170	T=0.7487	A=0.2513
1000Genomes_30x	American	Sub	980	T=0.770	A=0.230
1000Genomes	Global	Study-wide	5008	T=0.7516	A=0.2484
1000Genomes	African	Sub	1322	T=0.8888	A=0.1112
1000Genomes	East Asian	Sub	1008	T=0.7450	A=0.2550
1000Genomes	Europe	Sub	1006	T=0.7555	A=0.2445
1000Genomes	South Asian	Sub	978	T=0.554	A=0.446
1000Genomes	American	Sub	694	T=0.772	A=0.228
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.7656	A=0.2344
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.7514	A=0.2486
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.7430	A=0.2570
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.7778	A=0.2222
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.730	A=0.270
Northern Sweden	ACPOP	Study-wide	600	T=0.755	A=0.245
SGDP_PRJ	Global	Study-wide	304	T=0.372	A=0.628
Qatari	Global	Study-wide	216	T=0.620	A=0.380
A Vietnamese Genetic Variation Database	Global	Study-wide	214	T=0.724	A=0.276
The Danish reference pan genome	Danish	Study-wide	40	T=0.70	A=0.30
Siberian	Global	Study-wide	10	T=0.5	A=0.5

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 15	NC_000015.10:g.87278722T>A
GRCh38.p14 chr 15	NC_000015.10:g.87278722T>G
GRCh37.p13 chr 15	NC_000015.9:g.87821953T>A
GRCh37.p13 chr 15	NC_000015.9:g.87821953T>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	T=	A	G
GRCh38.p14 chr 15	NC_000015.10:g.87278722=	NC_000015.10:g.87278722T>A	NC_000015.10:g.87278722T>G
GRCh37.p13 chr 15	NC_000015.9:g.87821953=	NC_000015.9:g.87821953T>A	NC_000015.9:g.87821953T>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#.

51 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCMHGSC_JDW	ss90241565	Mar 24, 2008 (129)
2	GMI	ss282350727	May 04, 2012 (144)
3	GMI	ss286996487	Apr 25, 2013 (144)
4	PJP	ss291768776	May 09, 2011 (144)
5	1000GENOMES	ss338951233	May 09, 2011 (144)
6	SSMP	ss660371953	Apr 25, 2013 (144)
7	EVA-GONL	ss992047196	Aug 21, 2014 (144)
8	JMKIDD_LAB	ss1080311663	Aug 21, 2014 (144)
9	1000GENOMES	ss1354474643	Aug 21, 2014 (144)
10	DDI	ss1427705091	Apr 01, 2015 (144)
11	EVA_GENOME_DK	ss1577738676	Apr 01, 2015 (144)
12	EVA_UK10K_ALSPAC	ss1633539077	Apr 01, 2015 (144)
13	EVA_UK10K_TWINSUK	ss1676533110	Apr 01, 2015 (144)
14	EVA_DECODE	ss1696074242	Apr 01, 2015 (144)
15	WEILL_CORNELL_DGM	ss1935448084	Feb 12, 2016 (147)
16	JJLAB	ss2028507791	Sep 14, 2016 (149)
17	USC_VALOUEV	ss2156916515	Dec 20, 2016 (150)
18	HUMAN_LONGEVITY	ss2208824758	Dec 20, 2016 (150)
19	GRF	ss2701401631	Nov 08, 2017 (151)
20	GNOMAD	ss2937818348	Nov 08, 2017 (151)
21	SWEGEN	ss3013698906	Nov 08, 2017 (151)
22	CSHL	ss3351228297	Nov 08, 2017 (151)
23	URBANLAB	ss3650411677	Oct 12, 2018 (152)
24	EGCUT_WGS	ss3680828490	Jul 13, 2019 (153)
25	EVA_DECODE	ss3698391973	Jul 13, 2019 (153)
26	ACPOP	ss3741141714	Jul 13, 2019 (153)
27	EVA	ss3753401974	Jul 13, 2019 (153)
28	PACBIO	ss3787918540	Jul 13, 2019 (153)
29	PACBIO	ss3792919002	Jul 13, 2019 (153)
30	PACBIO	ss3797803608	Jul 13, 2019 (153)
31	KHV_HUMAN_GENOMES	ss3818703531	Jul 13, 2019 (153)
32	EVA	ss3834359056	Apr 27, 2020 (154)
33	EVA	ss3840782000	Apr 27, 2020 (154)
34	EVA	ss3846271912	Apr 27, 2020 (154)
35	SGDP_PRJ	ss3883450992	Apr 27, 2020 (154)
36	KRGDB	ss3932697282	Apr 27, 2020 (154)
37	KOGIC	ss3976667829	Apr 27, 2020 (154)
38	KOGIC	ss3976667830	Apr 27, 2020 (154)
39	TOPMED	ss5000288685	Apr 27, 2021 (155)
40	TOMMO_GENOMICS	ss5217390481	Apr 27, 2021 (155)
41	1000G_HIGH_COVERAGE	ss5299335017	Oct 16, 2022 (156)
42	HUGCELL_USP	ss5492960017	Oct 16, 2022 (156)
43	EVA	ss5511512166	Oct 16, 2022 (156)
44	1000G_HIGH_COVERAGE	ss5601184419	Oct 16, 2022 (156)
45	SANFORD_IMAGENETICS	ss5658010384	Oct 16, 2022 (156)
46	TOMMO_GENOMICS	ss5771558305	Oct 16, 2022 (156)
47	YY_MCH	ss5815559197	Oct 16, 2022 (156)
48	EVA	ss5828547297	Oct 16, 2022 (156)
49	EVA	ss5851395962	Oct 16, 2022 (156)
50	EVA	ss5876894338	Oct 16, 2022 (156)
51	EVA	ss5949431335	Oct 16, 2022 (156)
52	1000Genomes	NC_000015.9 - 87821953	Oct 12, 2018 (152)
53	1000Genomes_30x	NC_000015.10 - 87278722	Oct 16, 2022 (156)
54	The Avon Longitudinal Study of Parents and Children	NC_000015.9 - 87821953	Oct 12, 2018 (152)
55	Genetic variation in the Estonian population	NC_000015.9 - 87821953	Oct 12, 2018 (152)
56	The Danish reference pan genome	NC_000015.9 - 87821953	Apr 27, 2020 (154)
57	gnomAD - Genomes	NC_000015.10 - 87278722	Apr 27, 2021 (155)
58	Genome of the Netherlands Release 5	NC_000015.9 - 87821953	Apr 27, 2020 (154)
59	KOREAN population from KRGDB	NC_000015.9 - 87821953	Apr 27, 2020 (154)
60	Korean Genome Project Submission ignored due to conflicting rows: Row 33045830 (NC_000015.10:87278721:T:A 456/1832) Row 33045831 (NC_000015.10:87278721:T:G 1/1832)	-	Apr 27, 2020 (154)
61	Korean Genome Project Submission ignored due to conflicting rows: Row 33045830 (NC_000015.10:87278721:T:A 456/1832) Row 33045831 (NC_000015.10:87278721:T:G 1/1832)	-	Apr 27, 2020 (154)
62	Northern Sweden	NC_000015.9 - 87821953	Jul 13, 2019 (153)
63	Qatari	NC_000015.9 - 87821953	Apr 27, 2020 (154)
64	SGDP_PRJ	NC_000015.9 - 87821953	Apr 27, 2020 (154)
65	Siberian	NC_000015.9 - 87821953	Apr 27, 2020 (154)
66	8.3KJPN	NC_000015.9 - 87821953	Apr 27, 2021 (155)
67	14KJPN	NC_000015.10 - 87278722	Oct 16, 2022 (156)
68	TopMed	NC_000015.10 - 87278722	Apr 27, 2021 (155)
69	UK 10K study - Twins	NC_000015.9 - 87821953	Oct 12, 2018 (152)
70	A Vietnamese Genetic Variation Database	NC_000015.9 - 87821953	Jul 13, 2019 (153)
71	ALFA	NC_000015.10 - 87278722	Apr 27, 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)
rs4426326	Mar 11, 2006 (126)
rs138503136	Jul 01, 2015 (144)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss90241565, ss282350727, ss286996487, ss291768776, ss1696074242	NC_000015.8:85622956:T:A	NC_000015.10:87278721:T:A	(self)
67582579, 37532239, 26566738, 3958278, 16747649, 39874676, 14426579, 17490014, 35467972, 9432869, 75359788, 37532239, 8343263, ss338951233, ss660371953, ss992047196, ss1080311663, ss1354474643, ss1427705091, ss1577738676, ss1633539077, ss1676533110, ss1935448084, ss2028507791, ss2156916515, ss2701401631, ss2937818348, ss3013698906, ss3351228297, ss3680828490, ss3741141714, ss3753401974, ss3787918540, ss3792919002, ss3797803608, ss3834359056, ss3840782000, ss3883450992, ss3932697282, ss5217390481, ss5511512166, ss5658010384, ss5828547297, ss5949431335	NC_000015.9:87821952:T:A	NC_000015.10:87278721:T:A	(self)
88710354, 476504550, 105395409, 215834345, 1739533506, ss2208824758, ss3650411677, ss3698391973, ss3818703531, ss3846271912, ss3976667829, ss5000288685, ss5299335017, ss5492960017, ss5601184419, ss5771558305, ss5815559197, ss5851395962, ss5876894338	NC_000015.10:87278721:T:A	NC_000015.10:87278721:T:A	(self)
ss3976667830	NC_000015.10:87278721:T:G	NC_000015.10:87278721: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 rs2201961

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

rs2201961