Name: rs2338971
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.

rs2338971

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:101414449 (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>C / T>G
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.226333 (59908/264690, TOPMED)
T=0.210868 (29527/140026, GnomAD)
T=0.14825 (4189/28256, 14KJPN) (+ 15 more)
T=0.22264 (3950/17742, ALFA)
T=0.15042 (2521/16760, 8.3KJPN)
T=0.2359 (1511/6404, 1000G_30x)
T=0.2334 (1169/5008, 1000G)
T=0.2429 (1088/4480, Estonian)
T=0.2081 (802/3854, ALSPAC)
T=0.2006 (744/3708, TWINSUK)
T=0.2031 (595/2930, KOREAN)
T=0.1747 (320/1832, Korea1K)
T=0.194 (194/998, GoNL)
T=0.245 (147/600, NorthernSweden)
T=0.156 (78/500, SGDP_PRJ)
T=0.181 (39/216, Qatari)
T=0.17 (9/54, Siberian)
T=0.28 (11/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: None
Publications: 2 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	17742	T=0.22264	A=0.00000, C=0.77736
European	Sub	13654	T=0.21730	A=0.00000, C=0.78270
African	Sub	2434	T=0.1709	A=0.0000, C=0.8291
African Others	Sub	90	T=0.11	A=0.00, C=0.89
African American	Sub	2344	T=0.1732	A=0.0000, C=0.8268
Asian	Sub	112	T=0.232	A=0.000, C=0.768
East Asian	Sub	86	T=0.23	A=0.00, C=0.77
Other Asian	Sub	26	T=0.23	A=0.00, C=0.77
Latin American 1	Sub	146	T=0.219	A=0.000, C=0.781
Latin American 2	Sub	610	T=0.502	A=0.000, C=0.498
South Asian	Sub	98	T=0.35	A=0.00, C=0.65
Other	Sub	688	T=0.246	A=0.000, C=0.754

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").

Download

Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	T=0.226333	C=0.773667
gnomAD - Genomes	Global	Study-wide	140026	T=0.210868	C=0.789132
gnomAD - Genomes	European	Sub	75830	T=0.20804	C=0.79196
gnomAD - Genomes	African	Sub	41984	T=0.17161	C=0.82839
gnomAD - Genomes	American	Sub	13616	T=0.35106	C=0.64894
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	T=0.2086	C=0.7914
gnomAD - Genomes	East Asian	Sub	3124	T=0.1994	C=0.8006
gnomAD - Genomes	Other	Sub	2150	T=0.2093	C=0.7907
14KJPN	JAPANESE	Study-wide	28256	T=0.14825	C=0.85175
Allele Frequency Aggregator	Total	Global	17742	T=0.22264	A=0.00000, C=0.77736
Allele Frequency Aggregator	European	Sub	13654	T=0.21730	A=0.00000, C=0.78270
Allele Frequency Aggregator	African	Sub	2434	T=0.1709	A=0.0000, C=0.8291
Allele Frequency Aggregator	Other	Sub	688	T=0.246	A=0.000, C=0.754
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.502	A=0.000, C=0.498
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.219	A=0.000, C=0.781
Allele Frequency Aggregator	Asian	Sub	112	T=0.232	A=0.000, C=0.768
Allele Frequency Aggregator	South Asian	Sub	98	T=0.35	A=0.00, C=0.65
8.3KJPN	JAPANESE	Study-wide	16760	T=0.15042	C=0.84958
1000Genomes_30x	Global	Study-wide	6404	T=0.2359	C=0.7641
1000Genomes_30x	African	Sub	1786	T=0.1562	C=0.8438
1000Genomes_30x	Europe	Sub	1266	T=0.1690	C=0.8310
1000Genomes_30x	South Asian	Sub	1202	T=0.2862	C=0.7138
1000Genomes_30x	East Asian	Sub	1170	T=0.2000	C=0.8000
1000Genomes_30x	American	Sub	980	T=0.449	C=0.551
1000Genomes	Global	Study-wide	5008	T=0.2334	C=0.7666
1000Genomes	African	Sub	1322	T=0.1528	C=0.8472
1000Genomes	East Asian	Sub	1008	T=0.1994	C=0.8006
1000Genomes	Europe	Sub	1006	T=0.1710	C=0.8290
1000Genomes	South Asian	Sub	978	T=0.288	C=0.712
1000Genomes	American	Sub	694	T=0.450	C=0.550
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.2429	C=0.7571
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.2081	C=0.7919
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.2006	C=0.7994
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.2031	A=0.0000, C=0.7969, G=0.0000
Korean Genome Project	KOREAN	Study-wide	1832	T=0.1747	C=0.8253
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.194	C=0.806
Northern Sweden	ACPOP	Study-wide	600	T=0.245	C=0.755
SGDP_PRJ	Global	Study-wide	500	T=0.156	C=0.844
Qatari	Global	Study-wide	216	T=0.181	C=0.819
Siberian	Global	Study-wide	54	T=0.17	C=0.83
The Danish reference pan genome	Danish	Study-wide	40	T=0.28	C=0.72

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.101414449T>A
GRCh38.p14 chr 1	NC_000001.11:g.101414449T>C
GRCh38.p14 chr 1	NC_000001.11:g.101414449T>G
GRCh37.p13 chr 1	NC_000001.10:g.101880005T>A
GRCh37.p13 chr 1	NC_000001.10:g.101880005T>C
GRCh37.p13 chr 1	NC_000001.10:g.101880005T>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	C	G
GRCh38.p14 chr 1	NC_000001.11:g.101414449=	NC_000001.11:g.101414449T>A	NC_000001.11:g.101414449T>C	NC_000001.11:g.101414449T>G
GRCh37.p13 chr 1	NC_000001.10:g.101880005=	NC_000001.10:g.101880005T>A	NC_000001.10:g.101880005T>C	NC_000001.10:g.101880005T>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#.

77 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss3291856	Sep 28, 2001 (100)
2	SC_JCM	ss5951091	Feb 20, 2003 (126)
3	BCM_SSAHASNP	ss9810876	Jul 11, 2003 (116)
4	WI_SSAHASNP	ss11343865	Jul 11, 2003 (116)
5	CSHL-HAPMAP	ss16439643	Feb 27, 2004 (120)
6	CSHL-HAPMAP	ss19137218	Feb 27, 2004 (120)
7	CSHL-HAPMAP	ss19860755	Feb 27, 2004 (120)
8	SSAHASNP	ss20580434	Apr 05, 2004 (121)
9	ABI	ss41186720	Mar 10, 2006 (126)
10	HGSV	ss85987999	Dec 15, 2007 (130)
11	BCMHGSC_JDW	ss87664368	Mar 23, 2008 (129)
12	HUMANGENOME_JCVI	ss97962218	Feb 05, 2009 (130)
13	1000GENOMES	ss108463215	Jan 23, 2009 (130)
14	1000GENOMES	ss110909641	Jan 25, 2009 (130)
15	ILLUMINA-UK	ss118926785	Dec 01, 2009 (131)
16	COMPLETE_GENOMICS	ss163764008	Jul 04, 2010 (132)
17	COMPLETE_GENOMICS	ss164890493	Jul 04, 2010 (132)
18	COMPLETE_GENOMICS	ss166916469	Jul 04, 2010 (132)
19	BUSHMAN	ss198847234	Jul 04, 2010 (132)
20	BCM-HGSC-SUB	ss205109748	Jul 04, 2010 (132)
21	1000GENOMES	ss218555747	Jul 14, 2010 (132)
22	1000GENOMES	ss230661743	Jul 14, 2010 (132)
23	1000GENOMES	ss238327430	Jul 15, 2010 (132)
24	GMI	ss275949795	May 04, 2012 (137)
25	GMI	ss284108002	Apr 25, 2013 (138)
26	PJP	ss290582947	May 09, 2011 (134)
27	TISHKOFF	ss554493554	Apr 25, 2013 (138)
28	SSMP	ss648262649	Apr 25, 2013 (138)
29	EVA-GONL	ss975496081	Aug 21, 2014 (142)
30	JMKIDD_LAB	ss1068137267	Aug 21, 2014 (142)
31	1000GENOMES	ss1292156344	Aug 21, 2014 (142)
32	DDI	ss1425914901	Apr 01, 2015 (144)
33	EVA_GENOME_DK	ss1574279633	Apr 01, 2015 (144)
34	EVA_DECODE	ss1584874363	Apr 01, 2015 (144)
35	EVA_UK10K_ALSPAC	ss1600844079	Apr 01, 2015 (144)
36	EVA_UK10K_TWINSUK	ss1643838112	Apr 01, 2015 (144)
37	HAMMER_LAB	ss1794827657	Sep 08, 2015 (146)
38	WEILL_CORNELL_DGM	ss1918695510	Feb 12, 2016 (147)
39	GENOMED	ss1966823284	Jul 19, 2016 (147)
40	JJLAB	ss2019869744	Sep 14, 2016 (149)
41	USC_VALOUEV	ss2147888122	Dec 20, 2016 (150)
42	HUMAN_LONGEVITY	ss2165135703	Dec 20, 2016 (150)
43	SYSTEMSBIOZJU	ss2624445506	Nov 08, 2017 (151)
44	GRF	ss2697815819	Nov 08, 2017 (151)
45	GNOMAD	ss2758778776	Nov 08, 2017 (151)
46	SWEGEN	ss2987324956	Nov 08, 2017 (151)
47	BIOINF_KMB_FNS_UNIBA	ss3023698172	Nov 08, 2017 (151)
48	CSHL	ss3343601189	Nov 08, 2017 (151)
49	URBANLAB	ss3646734283	Oct 11, 2018 (152)
50	EGCUT_WGS	ss3655411601	Jul 12, 2019 (153)
51	EVA_DECODE	ss3687391630	Jul 12, 2019 (153)
52	ACPOP	ss3727324875	Jul 12, 2019 (153)
53	EVA	ss3746588638	Jul 12, 2019 (153)
54	PACBIO	ss3783499730	Jul 12, 2019 (153)
55	PACBIO	ss3789144053	Jul 12, 2019 (153)
56	PACBIO	ss3794016915	Jul 12, 2019 (153)
57	KHV_HUMAN_GENOMES	ss3799589094	Jul 12, 2019 (153)
58	EVA	ss3826333020	Apr 25, 2020 (154)
59	EVA	ss3836556484	Apr 25, 2020 (154)
60	EVA	ss3841964555	Apr 25, 2020 (154)
61	SGDP_PRJ	ss3849502647	Apr 25, 2020 (154)
62	KRGDB	ss3894583464	Apr 25, 2020 (154)
63	KOGIC	ss3945114353	Apr 25, 2020 (154)
64	TOPMED	ss4461141711	Apr 25, 2021 (155)
65	TOMMO_GENOMICS	ss5145368672	Apr 25, 2021 (155)
66	1000G_HIGH_COVERAGE	ss5243363801	Oct 12, 2022 (156)
67	HUGCELL_USP	ss5444312578	Oct 12, 2022 (156)
68	1000G_HIGH_COVERAGE	ss5516227662	Oct 12, 2022 (156)
69	SANFORD_IMAGENETICS	ss5624213550	Oct 12, 2022 (156)
70	SANFORD_IMAGENETICS	ss5626155796	Oct 12, 2022 (156)
71	TOMMO_GENOMICS	ss5670544050	Oct 12, 2022 (156)
72	YY_MCH	ss5800870083	Oct 12, 2022 (156)
73	EVA	ss5832388492	Oct 12, 2022 (156)
74	EVA	ss5849038858	Oct 12, 2022 (156)
75	EVA	ss5909522852	Oct 12, 2022 (156)
76	EVA	ss5938018602	Oct 12, 2022 (156)
77	EVA	ss5979283945	Oct 12, 2022 (156)
78	1000Genomes	NC_000001.10 - 101880005	Oct 11, 2018 (152)
79	1000Genomes_30x	NC_000001.11 - 101414449	Oct 12, 2022 (156)
80	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 101880005	Oct 11, 2018 (152)
81	Genetic variation in the Estonian population	NC_000001.10 - 101880005	Oct 11, 2018 (152)
82	The Danish reference pan genome	NC_000001.10 - 101880005	Apr 25, 2020 (154)
83	gnomAD - Genomes	NC_000001.11 - 101414449	Apr 25, 2021 (155)
84	Genome of the Netherlands Release 5	NC_000001.10 - 101880005	Apr 25, 2020 (154)
85	KOREAN population from KRGDB	NC_000001.10 - 101880005	Apr 25, 2020 (154)
86	Korean Genome Project	NC_000001.11 - 101414449	Apr 25, 2020 (154)
87	Northern Sweden	NC_000001.10 - 101880005	Jul 12, 2019 (153)
88	Qatari	NC_000001.10 - 101880005	Apr 25, 2020 (154)
89	SGDP_PRJ	NC_000001.10 - 101880005	Apr 25, 2020 (154)
90	Siberian	NC_000001.10 - 101880005	Apr 25, 2020 (154)
91	8.3KJPN	NC_000001.10 - 101880005	Apr 25, 2021 (155)
92	14KJPN	NC_000001.11 - 101414449	Oct 12, 2022 (156)
93	TopMed	NC_000001.11 - 101414449	Apr 25, 2021 (155)
94	UK 10K study - Twins	NC_000001.10 - 101880005	Oct 11, 2018 (152)
95	ALFA	NC_000001.11 - 101414449	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)
rs4439370	Mar 10, 2006 (126)
rs59350353	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
1760858, ss3894583464	NC_000001.10:101880004:T:A	NC_000001.11:101414448:T:A	(self)
1982674637	NC_000001.11:101414448:T:A	NC_000001.11:101414448:T:A	(self)
ss85987999	NC_000001.8:101592025:T:C	NC_000001.11:101414448:T:C	(self)
ss87664368, ss108463215, ss110909641, ss118926785, ss163764008, ss164890493, ss166916469, ss198847234, ss205109748, ss275949795, ss284108002, ss290582947, ss1584874363	NC_000001.9:101652592:T:C	NC_000001.11:101414448:T:C	(self)
2921802, 1613749, 1149849, 1633863, 699878, 1760858, 609740, 737440, 1519627, 404476, 3337979, 1613749, ss218555747, ss230661743, ss238327430, ss554493554, ss648262649, ss975496081, ss1068137267, ss1292156344, ss1425914901, ss1574279633, ss1600844079, ss1643838112, ss1794827657, ss1918695510, ss1966823284, ss2019869744, ss2147888122, ss2624445506, ss2697815819, ss2758778776, ss2987324956, ss3343601189, ss3655411601, ss3727324875, ss3746588638, ss3783499730, ss3789144053, ss3794016915, ss3826333020, ss3836556484, ss3849502647, ss3894583464, ss5145368672, ss5624213550, ss5626155796, ss5832388492, ss5938018602, ss5979283945	NC_000001.10:101880004:T:C	NC_000001.11:101414448:T:C	(self)
3753597, 20660815, 1492354, 4381154, 24748046, 1982674637, ss2165135703, ss3023698172, ss3646734283, ss3687391630, ss3799589094, ss3841964555, ss3945114353, ss4461141711, ss5243363801, ss5444312578, ss5516227662, ss5670544050, ss5800870083, ss5849038858, ss5909522852	NC_000001.11:101414448:T:C	NC_000001.11:101414448:T:C	(self)
ss9810876, ss11343865	NT_028050.12:2753675:T:C	NC_000001.11:101414448:T:C	(self)
ss16439643, ss19137218, ss19860755, ss20580434	NT_028050.13:10068948:T:C	NC_000001.11:101414448:T:C	(self)
ss3291856, ss5951091, ss41186720, ss97962218	NT_032977.9:71851922:T:C	NC_000001.11:101414448:T:C	(self)
1760858, ss3894583464	NC_000001.10:101880004:T:G	NC_000001.11:101414448:T:G	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

2 citations for rs2338971

PMID	Title	Author	Year	Journal
24511991	Identification of a novel Parkinson's disease locus via stratified genome-wide association study.	Hill-Burns EM et al.	2014	BMC genomics
26732583	The analysis of association between SNCA, HUSEYO and CSMD1 gene variants and Parkinson's disease in Iranian population.	Shahmohammadibeni N et al.	2016	Neurological sciences

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

rs2338971