Name: rs3131502
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.

rs3131502

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:24739957 (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
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.314194 (83164/264690, TOPMED)
T=0.307989 (43111/139976, GnomAD)
T=0.31024 (9715/31314, ALFA) (+ 17 more)
T=0.46196 (13054/28258, 14KJPN)
T=0.45907 (7694/16760, 8.3KJPN)
T=0.3901 (2498/6404, 1000G_30x)
T=0.3864 (1935/5008, 1000G)
T=0.3145 (1409/4480, Estonian)
T=0.2867 (1105/3854, ALSPAC)
T=0.2783 (1032/3708, TWINSUK)
T=0.4587 (1344/2930, KOREAN)
T=0.3732 (706/1892, HapMap)
T=0.4618 (846/1832, Korea1K)
T=0.281 (280/998, GoNL)
T=0.295 (177/600, NorthernSweden)
T=0.268 (121/452, SGDP_PRJ)
C=0.426 (92/216, Qatari)
C=0.444 (96/216, Vietnamese)
T=0.17 (9/52, Siberian)
T=0.23 (9/40, 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	31314	T=0.31024	C=0.68976
European	Sub	19066	T=0.30300	C=0.69700
African	Sub	7390	T=0.3396	C=0.6604
African Others	Sub	244	T=0.336	C=0.664
African American	Sub	7146	T=0.3398	C=0.6602
Asian	Sub	164	T=0.402	C=0.598
East Asian	Sub	110	T=0.455	C=0.545
Other Asian	Sub	54	T=0.30	C=0.70
Latin American 1	Sub	306	T=0.294	C=0.706
Latin American 2	Sub	2820	T=0.2709	C=0.7291
South Asian	Sub	110	T=0.482	C=0.518
Other	Sub	1458	T=0.3121	C=0.6879

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=0.314194	C=0.685806
gnomAD - Genomes	Global	Study-wide	139976	T=0.307989	C=0.692011
gnomAD - Genomes	European	Sub	75862	T=0.28826	C=0.71174
gnomAD - Genomes	African	Sub	41888	T=0.33305	C=0.66695
gnomAD - Genomes	American	Sub	13634	T=0.27189	C=0.72811
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	T=0.4116	C=0.5884
gnomAD - Genomes	East Asian	Sub	3120	T=0.4984	C=0.5016
gnomAD - Genomes	Other	Sub	2148	T=0.3082	C=0.6918
Allele Frequency Aggregator	Total	Global	31314	T=0.31024	C=0.68976
Allele Frequency Aggregator	European	Sub	19066	T=0.30300	C=0.69700
Allele Frequency Aggregator	African	Sub	7390	T=0.3396	C=0.6604
Allele Frequency Aggregator	Latin American 2	Sub	2820	T=0.2709	C=0.7291
Allele Frequency Aggregator	Other	Sub	1458	T=0.3121	C=0.6879
Allele Frequency Aggregator	Latin American 1	Sub	306	T=0.294	C=0.706
Allele Frequency Aggregator	Asian	Sub	164	T=0.402	C=0.598
Allele Frequency Aggregator	South Asian	Sub	110	T=0.482	C=0.518
14KJPN	JAPANESE	Study-wide	28258	T=0.46196	C=0.53804
8.3KJPN	JAPANESE	Study-wide	16760	T=0.45907	C=0.54093
1000Genomes_30x	Global	Study-wide	6404	T=0.3901	C=0.6099
1000Genomes_30x	African	Sub	1786	T=0.3875	C=0.6125
1000Genomes_30x	Europe	Sub	1266	T=0.3025	C=0.6975
1000Genomes_30x	South Asian	Sub	1202	T=0.4692	C=0.5308
1000Genomes_30x	East Asian	Sub	1170	T=0.4906	C=0.5094
1000Genomes_30x	American	Sub	980	T=0.291	C=0.709
1000Genomes	Global	Study-wide	5008	T=0.3864	C=0.6136
1000Genomes	African	Sub	1322	T=0.3820	C=0.6180
1000Genomes	East Asian	Sub	1008	T=0.4861	C=0.5139
1000Genomes	Europe	Sub	1006	T=0.3012	C=0.6988
1000Genomes	South Asian	Sub	978	T=0.457	C=0.543
1000Genomes	American	Sub	694	T=0.274	C=0.726
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.3145	C=0.6855
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.2867	C=0.7133
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.2783	C=0.7217
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.4587	A=0.0000, C=0.5413
HapMap	Global	Study-wide	1892	T=0.3732	C=0.6268
HapMap	American	Sub	770	T=0.344	C=0.656
HapMap	African	Sub	692	T=0.382	C=0.618
HapMap	Asian	Sub	254	T=0.465	C=0.535
HapMap	Europe	Sub	176	T=0.335	C=0.665
Korean Genome Project	KOREAN	Study-wide	1832	T=0.4618	C=0.5382
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.281	C=0.719
Northern Sweden	ACPOP	Study-wide	600	T=0.295	C=0.705
SGDP_PRJ	Global	Study-wide	452	T=0.268	C=0.732
Qatari	Global	Study-wide	216	T=0.574	C=0.426
A Vietnamese Genetic Variation Database	Global	Study-wide	216	T=0.556	C=0.444
Siberian	Global	Study-wide	52	T=0.17	C=0.83
The Danish reference pan genome	Danish	Study-wide	40	T=0.23	C=0.78

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.24739957T>A
GRCh38.p14 chr 1	NC_000001.11:g.24739957T>C
GRCh37.p13 chr 1	NC_000001.10:g.25066448T>A
GRCh37.p13 chr 1	NC_000001.10:g.25066448T>C

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
GRCh38.p14 chr 1	NC_000001.11:g.24739957=	NC_000001.11:g.24739957T>A	NC_000001.11:g.24739957T>C
GRCh37.p13 chr 1	NC_000001.10:g.25066448=	NC_000001.10:g.25066448T>A	NC_000001.10:g.25066448T>C

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#.

94 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss4378923	Mar 26, 2002 (103)
2	WI_SSAHASNP	ss11417512	Jul 11, 2003 (116)
3	SC_SNP	ss13052242	Dec 05, 2003 (119)
4	CSHL-HAPMAP	ss16384093	Feb 27, 2004 (120)
5	CSHL-HAPMAP	ss19829349	Feb 27, 2004 (120)
6	SSAHASNP	ss20429220	Apr 05, 2004 (121)
7	ABI	ss44004466	Mar 13, 2006 (126)
8	AFFY	ss66291092	Dec 01, 2006 (127)
9	ILLUMINA	ss75164189	Dec 06, 2007 (129)
10	AFFY	ss75955727	Dec 08, 2007 (130)
11	HGSV	ss78603870	Dec 06, 2007 (129)
12	KRIBB_YJKIM	ss81938423	Dec 15, 2007 (130)
13	HGSV	ss85944173	Dec 14, 2007 (130)
14	BCMHGSC_JDW	ss87308389	Mar 23, 2008 (129)
15	HUMANGENOME_JCVI	ss97926192	Feb 03, 2009 (130)
16	BGI	ss102728780	Dec 01, 2009 (131)
17	1000GENOMES	ss108069458	Jan 22, 2009 (130)
18	1000GENOMES	ss110197439	Jan 24, 2009 (130)
19	ILLUMINA-UK	ss118569807	Feb 14, 2009 (130)
20	ENSEMBL	ss137850019	Dec 01, 2009 (131)
21	ENSEMBL	ss138991581	Dec 01, 2009 (131)
22	GMI	ss154784299	Dec 01, 2009 (131)
23	COMPLETE_GENOMICS	ss163195189	Jul 04, 2010 (132)
24	COMPLETE_GENOMICS	ss163993230	Jul 04, 2010 (132)
25	COMPLETE_GENOMICS	ss166255821	Jul 04, 2010 (132)
26	AFFY	ss169644039	Jul 04, 2010 (132)
27	ILLUMINA	ss173568080	Jul 04, 2010 (132)
28	BUSHMAN	ss198184409	Jul 04, 2010 (132)
29	BCM-HGSC-SUB	ss205266882	Jul 04, 2010 (132)
30	1000GENOMES	ss218287713	Jul 14, 2010 (132)
31	1000GENOMES	ss230465587	Jul 14, 2010 (132)
32	1000GENOMES	ss238172430	Jul 15, 2010 (132)
33	BL	ss252991137	May 09, 2011 (134)
34	GMI	ss275756809	May 04, 2012 (137)
35	GMI	ss284020792	Apr 25, 2013 (138)
36	PJP	ss290788292	May 09, 2011 (134)
37	ILLUMINA	ss537164955	Sep 08, 2015 (146)
38	TISHKOFF	ss553902739	Apr 25, 2013 (138)
39	SSMP	ss647645907	Apr 25, 2013 (138)
40	EVA-GONL	ss974956215	Aug 21, 2014 (142)
41	JMKIDD_LAB	ss1067741510	Aug 21, 2014 (142)
42	1000GENOMES	ss1290073100	Aug 21, 2014 (142)
43	DDI	ss1425748977	Apr 01, 2015 (144)
44	EVA_GENOME_DK	ss1573946980	Apr 01, 2015 (144)
45	EVA_DECODE	ss1584315133	Apr 01, 2015 (144)
46	EVA_UK10K_ALSPAC	ss1599746217	Apr 01, 2015 (144)
47	EVA_UK10K_TWINSUK	ss1642740250	Apr 01, 2015 (144)
48	EVA_SVP	ss1712318638	Apr 01, 2015 (144)
49	HAMMER_LAB	ss1794076608	Sep 08, 2015 (146)
50	WEILL_CORNELL_DGM	ss1918167867	Feb 12, 2016 (147)
51	GENOMED	ss1966707030	Jul 19, 2016 (147)
52	JJLAB	ss2019596117	Sep 14, 2016 (149)
53	USC_VALOUEV	ss2147602106	Dec 20, 2016 (150)
54	HUMAN_LONGEVITY	ss2160804628	Dec 20, 2016 (150)
55	SYSTEMSBIOZJU	ss2624314977	Nov 08, 2017 (151)
56	GRF	ss2697507516	Nov 08, 2017 (151)
57	GNOMAD	ss2752776179	Nov 08, 2017 (151)
58	AFFY	ss2985503242	Nov 08, 2017 (151)
59	SWEGEN	ss2986482387	Nov 08, 2017 (151)
60	BIOINF_KMB_FNS_UNIBA	ss3023563892	Nov 08, 2017 (151)
61	CSHL	ss3343371872	Nov 08, 2017 (151)
62	ILLUMINA	ss3626050825	Oct 11, 2018 (152)
63	ILLUMINA	ss3637743677	Oct 11, 2018 (152)
64	ILLUMINA	ss3642756942	Oct 11, 2018 (152)
65	URBANLAB	ss3646625438	Oct 11, 2018 (152)
66	EGCUT_WGS	ss3654549030	Jul 12, 2019 (153)
67	EVA_DECODE	ss3686367202	Jul 12, 2019 (153)
68	ACPOP	ss3726877645	Jul 12, 2019 (153)
69	EVA	ss3745952191	Jul 12, 2019 (153)
70	PACBIO	ss3783356521	Jul 12, 2019 (153)
71	PACBIO	ss3789025608	Jul 12, 2019 (153)
72	PACBIO	ss3793898123	Jul 12, 2019 (153)
73	KHV_HUMAN_GENOMES	ss3798972430	Jul 12, 2019 (153)
74	EVA	ss3826076503	Apr 25, 2020 (154)
75	EVA	ss3836426371	Apr 25, 2020 (154)
76	EVA	ss3841831140	Apr 25, 2020 (154)
77	SGDP_PRJ	ss3848429263	Apr 25, 2020 (154)
78	KRGDB	ss3893347978	Apr 25, 2020 (154)
79	KOGIC	ss3944057354	Apr 25, 2020 (154)
80	EVA	ss4016898799	Apr 25, 2021 (155)
81	TOPMED	ss4442470182	Apr 25, 2021 (155)
82	TOMMO_GENOMICS	ss5142976388	Apr 25, 2021 (155)
83	1000G_HIGH_COVERAGE	ss5241545219	Oct 13, 2022 (156)
84	EVA	ss5317397730	Oct 13, 2022 (156)
85	HUGCELL_USP	ss5442690585	Oct 13, 2022 (156)
86	EVA	ss5505792286	Oct 13, 2022 (156)
87	1000G_HIGH_COVERAGE	ss5513467955	Oct 13, 2022 (156)
88	SANFORD_IMAGENETICS	ss5625130922	Oct 13, 2022 (156)
89	TOMMO_GENOMICS	ss5667432185	Oct 13, 2022 (156)
90	YY_MCH	ss5800421132	Oct 13, 2022 (156)
91	EVA	ss5831682711	Oct 13, 2022 (156)
92	EVA	ss5848826861	Oct 13, 2022 (156)
93	EVA	ss5907435734	Oct 13, 2022 (156)
94	EVA	ss5936947659	Oct 13, 2022 (156)
95	1000Genomes	NC_000001.10 - 25066448	Oct 11, 2018 (152)
96	1000Genomes_30x	NC_000001.11 - 24739957	Oct 13, 2022 (156)
97	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 25066448	Oct 11, 2018 (152)
98	Genetic variation in the Estonian population	NC_000001.10 - 25066448	Oct 11, 2018 (152)
99	The Danish reference pan genome	NC_000001.10 - 25066448	Apr 25, 2020 (154)
100	gnomAD - Genomes	NC_000001.11 - 24739957	Apr 25, 2021 (155)
101	Genome of the Netherlands Release 5	NC_000001.10 - 25066448	Apr 25, 2020 (154)
102	HapMap	NC_000001.11 - 24739957	Apr 25, 2020 (154)
103	KOREAN population from KRGDB	NC_000001.10 - 25066448	Apr 25, 2020 (154)
104	Korean Genome Project	NC_000001.11 - 24739957	Apr 25, 2020 (154)
105	Northern Sweden	NC_000001.10 - 25066448	Jul 12, 2019 (153)
106	Qatari	NC_000001.10 - 25066448	Apr 25, 2020 (154)
107	SGDP_PRJ	NC_000001.10 - 25066448	Apr 25, 2020 (154)
108	Siberian	NC_000001.10 - 25066448	Apr 25, 2020 (154)
109	8.3KJPN	NC_000001.10 - 25066448	Apr 25, 2021 (155)
110	14KJPN	NC_000001.11 - 24739957	Oct 13, 2022 (156)
111	TopMed	NC_000001.11 - 24739957	Apr 25, 2021 (155)
112	UK 10K study - Twins	NC_000001.10 - 25066448	Oct 11, 2018 (152)
113	A Vietnamese Genetic Variation Database	NC_000001.10 - 25066448	Jul 12, 2019 (153)
114	ALFA	NC_000001.11 - 24739957	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)
rs56487114	May 23, 2008 (130)
rs56979426	May 23, 2008 (130)
rs59391499	Feb 26, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
525372, ss3893347978	NC_000001.10:25066447:T:A	NC_000001.11:24739956:T:A	(self)
ss78603870, ss85944173	NC_000001.8:24811753:T:C	NC_000001.11:24739956:T:C	(self)
ss87308389, ss108069458, ss110197439, ss118569807, ss163195189, ss163993230, ss166255821, ss198184409, ss205266882, ss252991137, ss275756809, ss284020792, ss290788292, ss1584315133, ss1712318638, ss3642756942	NC_000001.9:24939034:T:C	NC_000001.11:24739956:T:C	(self)
762534, 405472, 287278, 1429607, 175891, 525372, 162510, 209797, 446243, 118460, 945695, 405472, 85604, ss218287713, ss230465587, ss238172430, ss537164955, ss553902739, ss647645907, ss974956215, ss1067741510, ss1290073100, ss1425748977, ss1573946980, ss1599746217, ss1642740250, ss1794076608, ss1918167867, ss1966707030, ss2019596117, ss2147602106, ss2624314977, ss2697507516, ss2752776179, ss2985503242, ss2986482387, ss3343371872, ss3626050825, ss3637743677, ss3654549030, ss3726877645, ss3745952191, ss3783356521, ss3789025608, ss3793898123, ss3826076503, ss3836426371, ss3848429263, ss3893347978, ss4016898799, ss5142976388, ss5317397730, ss5505792286, ss5625130922, ss5831682711, ss5936947659	NC_000001.10:25066447:T:C	NC_000001.11:24739956:T:C	(self)
993890, 5332241, 31834, 435355, 1269289, 6076517, 2626983928, ss2160804628, ss3023563892, ss3646625438, ss3686367202, ss3798972430, ss3841831140, ss3944057354, ss4442470182, ss5241545219, ss5442690585, ss5513467955, ss5667432185, ss5800421132, ss5848826861, ss5907435734	NC_000001.11:24739956:T:C	NC_000001.11:24739956:T:C	(self)
ss4378923, ss44004466, ss66291092, ss75164189, ss75955727, ss81938423, ss97926192, ss102728780, ss137850019, ss138991581, ss154784299, ss169644039, ss173568080	NT_004610.19:11746535:T:C	NC_000001.11:24739956:T:C	(self)
ss16384093, ss19829349, ss20429220	NT_077383.3:702672:T:C	NC_000001.11:24739956:T:C	(self)
ss11417512, ss13052242	NT_077961.1:154736:T:C	NC_000001.11:24739956:T:C	(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 rs3131502

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

rs3131502