Name: rs2532086
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.

rs2532086

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:15878641 (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=0.236564 (62616/264690, TOPMED)
G=0.226211 (31689/140086, GnomAD)
G=0.41868 (11831/28258, 14KJPN) (+ 16 more)
G=0.42064 (7050/16760, 8.3KJPN)
G=0.2198 (1915/8712, ALFA)
G=0.2814 (1802/6404, 1000G_30x)
G=0.2813 (1409/5008, 1000G)
G=0.1388 (622/4480, Estonian)
G=0.1832 (706/3854, ALSPAC)
G=0.1915 (710/3708, TWINSUK)
G=0.4253 (1246/2930, KOREAN)
G=0.182 (182/998, GoNL)
G=0.218 (131/600, NorthernSweden)
T=0.013 (7/534, MGP)
G=0.249 (119/478, SGDP_PRJ)
G=0.324 (70/216, Qatari)
G=0.346 (74/214, Vietnamese)
G=0.19 (10/54, Siberian)
G=0.28 (11/40, 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	8712	G=0.2198	C=0.0000, T=0.7802
European	Sub	7572	G=0.1900	C=0.0000, T=0.8100
African	Sub	816	G=0.409	C=0.000, T=0.591
African Others	Sub	46	G=0.63	C=0.00, T=0.37
African American	Sub	770	G=0.396	C=0.000, T=0.604
Asian	Sub	24	G=0.96	C=0.00, T=0.04
East Asian	Sub	16	G=1.00	C=0.00, T=0.00
Other Asian	Sub	8	G=0.9	C=0.0, T=0.1
Latin American 1	Sub	8	G=1.0	C=0.0, T=0.0
Latin American 2	Sub	26	G=1.00	C=0.00, T=0.00
South Asian	Sub	16	G=0.88	C=0.00, T=0.12
Other	Sub	250	G=0.284	C=0.000, T=0.716

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=0.236564	T=0.763436
gnomAD - Genomes	Global	Study-wide	140086	G=0.226211	T=0.773789
gnomAD - Genomes	European	Sub	75880	G=0.19161	T=0.80839
gnomAD - Genomes	African	Sub	41970	G=0.26297	T=0.73703
gnomAD - Genomes	American	Sub	13640	G=0.26217	T=0.73783
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	G=0.2595	T=0.7405
gnomAD - Genomes	East Asian	Sub	3126	G=0.3682	T=0.6318
gnomAD - Genomes	Other	Sub	2152	G=0.2440	T=0.7560
14KJPN	JAPANESE	Study-wide	28258	G=0.41868	T=0.58132
8.3KJPN	JAPANESE	Study-wide	16760	G=0.42064	T=0.57936
Allele Frequency Aggregator	Total	Global	8712	G=0.2198	C=0.0000, T=0.7802
Allele Frequency Aggregator	European	Sub	7572	G=0.1900	C=0.0000, T=0.8100
Allele Frequency Aggregator	African	Sub	816	G=0.409	C=0.000, T=0.591
Allele Frequency Aggregator	Other	Sub	250	G=0.284	C=0.000, T=0.716
Allele Frequency Aggregator	Latin American 2	Sub	26	G=1.00	C=0.00, T=0.00
Allele Frequency Aggregator	Asian	Sub	24	G=0.96	C=0.00, T=0.04
Allele Frequency Aggregator	South Asian	Sub	16	G=0.88	C=0.00, T=0.12
Allele Frequency Aggregator	Latin American 1	Sub	8	G=1.0	C=0.0, T=0.0
1000Genomes_30x	Global	Study-wide	6404	G=0.2814	T=0.7186
1000Genomes_30x	African	Sub	1786	G=0.2912	T=0.7088
1000Genomes_30x	Europe	Sub	1266	G=0.1935	T=0.8065
1000Genomes_30x	South Asian	Sub	1202	G=0.3095	T=0.6905
1000Genomes_30x	East Asian	Sub	1170	G=0.3803	T=0.6197
1000Genomes_30x	American	Sub	980	G=0.224	T=0.776
1000Genomes	Global	Study-wide	5008	G=0.2813	T=0.7187
1000Genomes	African	Sub	1322	G=0.2806	T=0.7194
1000Genomes	East Asian	Sub	1008	G=0.3829	T=0.6171
1000Genomes	Europe	Sub	1006	G=0.1918	T=0.8082
1000Genomes	South Asian	Sub	978	G=0.311	T=0.689
1000Genomes	American	Sub	694	G=0.223	T=0.777
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.1388	T=0.8612
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.1832	T=0.8168
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.1915	T=0.8085
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.4253	C=0.0000, T=0.5747
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.182	T=0.818
Northern Sweden	ACPOP	Study-wide	600	G=0.218	T=0.782
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	G=0.987	T=0.013
SGDP_PRJ	Global	Study-wide	478	G=0.249	T=0.751
Qatari	Global	Study-wide	216	G=0.324	T=0.676
A Vietnamese Genetic Variation Database	Global	Study-wide	214	G=0.346	T=0.654
Siberian	Global	Study-wide	54	G=0.19	T=0.81
The Danish reference pan genome	Danish	Study-wide	40	G=0.28	T=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 4	NC_000004.12:g.15878641G>C
GRCh38.p14 chr 4	NC_000004.12:g.15878641G>T
GRCh37.p13 chr 4	NC_000004.11:g.15880264G>C
GRCh37.p13 chr 4	NC_000004.11:g.15880264G>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 4	NC_000004.12:g.15878641=	NC_000004.12:g.15878641G>C	NC_000004.12:g.15878641G>T
GRCh37.p13 chr 4	NC_000004.11:g.15880264=	NC_000004.11:g.15880264G>C	NC_000004.11:g.15880264G>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#.

67 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss3549650	Sep 28, 2001 (100)
2	WI_SSAHASNP	ss6471365	Feb 20, 2003 (111)
3	WI_SSAHASNP	ss11647000	Jul 11, 2003 (116)
4	SC_SNP	ss15686720	Feb 27, 2004 (120)
5	CSHL-HAPMAP	ss19565685	Feb 27, 2004 (120)
6	SSAHASNP	ss22112893	Apr 05, 2004 (121)
7	HGSV	ss83655112	Dec 15, 2007 (130)
8	HGSV	ss83951696	Dec 15, 2007 (130)
9	BCMHGSC_JDW	ss92484636	Mar 24, 2008 (129)
10	HUMANGENOME_JCVI	ss98805143	Feb 05, 2009 (130)
11	ILLUMINA-UK	ss116888068	Feb 14, 2009 (130)
12	COMPLETE_GENOMICS	ss166213429	Jul 04, 2010 (132)
13	BUSHMAN	ss198106247	Jul 04, 2010 (132)
14	BCM-HGSC-SUB	ss206577656	Jul 04, 2010 (132)
15	BL	ss252957855	May 09, 2011 (134)
16	GMI	ss277590738	May 04, 2012 (137)
17	GMI	ss284853977	Apr 25, 2013 (138)
18	PJP	ss293294293	May 09, 2011 (134)
19	1000GENOMES	ss331462771	May 09, 2011 (134)
20	TISHKOFF	ss557337593	Apr 25, 2013 (138)
21	SSMP	ss651102337	Apr 25, 2013 (138)
22	EVA-GONL	ss979809627	Aug 21, 2014 (142)
23	JMKIDD_LAB	ss1071307089	Aug 21, 2014 (142)
24	1000GENOMES	ss1308598106	Aug 21, 2014 (142)
25	DDI	ss1429787424	Apr 01, 2015 (144)
26	EVA_GENOME_DK	ss1580432782	Apr 01, 2015 (144)
27	EVA_DECODE	ss1589298274	Apr 01, 2015 (144)
28	EVA_UK10K_ALSPAC	ss1609495460	Apr 01, 2015 (144)
29	EVA_UK10K_TWINSUK	ss1652489493	Apr 01, 2015 (144)
30	EVA_MGP	ss1711054560	Apr 01, 2015 (144)
31	HAMMER_LAB	ss1801060932	Sep 08, 2015 (146)
32	WEILL_CORNELL_DGM	ss1923048098	Feb 12, 2016 (147)
33	GENOMED	ss1969668873	Sep 14, 2016 (149)
34	JJLAB	ss2022097125	Sep 14, 2016 (149)
35	USC_VALOUEV	ss2150207600	Dec 20, 2016 (150)
36	HUMAN_LONGEVITY	ss2260737615	Dec 20, 2016 (150)
37	SYSTEMSBIOZJU	ss2625549584	Nov 08, 2017 (151)
38	GRF	ss2705651813	Nov 08, 2017 (151)
39	GNOMAD	ss2806099344	Nov 08, 2017 (151)
40	SWEGEN	ss2994208831	Nov 08, 2017 (151)
41	BIOINF_KMB_FNS_UNIBA	ss3024817721	Nov 08, 2017 (151)
42	CSHL	ss3345565369	Nov 08, 2017 (151)
43	URBANLAB	ss3647661883	Oct 12, 2018 (152)
44	EGCUT_WGS	ss3662116609	Jul 13, 2019 (153)
45	EVA_DECODE	ss3711488232	Jul 13, 2019 (153)
46	ACPOP	ss3730892982	Jul 13, 2019 (153)
47	EVA	ss3761449822	Jul 13, 2019 (153)
48	PACBIO	ss3784630828	Jul 13, 2019 (153)
49	PACBIO	ss3790099944	Jul 13, 2019 (153)
50	PACBIO	ss3794974997	Jul 13, 2019 (153)
51	KHV_HUMAN_GENOMES	ss3804583598	Jul 13, 2019 (153)
52	EVA	ss3828391442	Apr 26, 2020 (154)
53	EVA	ss3837629262	Apr 26, 2020 (154)
54	EVA	ss3843063449	Apr 26, 2020 (154)
55	SGDP_PRJ	ss3858311306	Apr 26, 2020 (154)
56	KRGDB	ss3904460446	Apr 26, 2020 (154)
57	TOPMED	ss4604243723	Apr 26, 2021 (155)
58	TOMMO_GENOMICS	ss5164388219	Apr 26, 2021 (155)
59	1000G_HIGH_COVERAGE	ss5258191522	Oct 17, 2022 (156)
60	HUGCELL_USP	ss5457074639	Oct 17, 2022 (156)
61	1000G_HIGH_COVERAGE	ss5538702154	Oct 17, 2022 (156)
62	SANFORD_IMAGENETICS	ss5634434729	Oct 17, 2022 (156)
63	TOMMO_GENOMICS	ss5698089664	Oct 17, 2022 (156)
64	YY_MCH	ss5804795004	Oct 17, 2022 (156)
65	EVA	ss5843609325	Oct 17, 2022 (156)
66	EVA	ss5862311525	Oct 17, 2022 (156)
67	EVA	ss5962812369	Oct 17, 2022 (156)
68	1000Genomes	NC_000004.11 - 15880264	Oct 12, 2018 (152)
69	1000Genomes_30x	NC_000004.12 - 15878641	Oct 17, 2022 (156)
70	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 15880264	Oct 12, 2018 (152)
71	Genetic variation in the Estonian population	NC_000004.11 - 15880264	Oct 12, 2018 (152)
72	The Danish reference pan genome	NC_000004.11 - 15880264	Apr 26, 2020 (154)
73	gnomAD - Genomes	NC_000004.12 - 15878641	Apr 26, 2021 (155)
74	Genome of the Netherlands Release 5	NC_000004.11 - 15880264	Apr 26, 2020 (154)
75	KOREAN population from KRGDB	NC_000004.11 - 15880264	Apr 26, 2020 (154)
76	Medical Genome Project healthy controls from Spanish population	NC_000004.11 - 15880264	Apr 26, 2020 (154)
77	Northern Sweden	NC_000004.11 - 15880264	Jul 13, 2019 (153)
78	Qatari	NC_000004.11 - 15880264	Apr 26, 2020 (154)
79	SGDP_PRJ	NC_000004.11 - 15880264	Apr 26, 2020 (154)
80	Siberian	NC_000004.11 - 15880264	Apr 26, 2020 (154)
81	8.3KJPN	NC_000004.11 - 15880264	Apr 26, 2021 (155)
82	14KJPN	NC_000004.12 - 15878641	Oct 17, 2022 (156)
83	TopMed	NC_000004.12 - 15878641	Apr 26, 2021 (155)
84	UK 10K study - Twins	NC_000004.11 - 15880264	Oct 12, 2018 (152)
85	A Vietnamese Genetic Variation Database	NC_000004.11 - 15880264	Jul 13, 2019 (153)
86	ALFA	NC_000004.12 - 15878641	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)
rs59396339	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
11637840, ss3904460446	NC_000004.11:15880263:G:C	NC_000004.12:15878640:G:C	(self)
10726194396	NC_000004.12:15878640:G:C	NC_000004.12:15878640:G:C	(self)
ss83655112, ss83951696	NC_000004.9:15556532:G:T	NC_000004.12:15878640:G:T	(self)
ss92484636, ss116888068, ss166213429, ss198106247, ss206577656, ss252957855, ss277590738, ss284853977, ss293294293, ss1589298274	NC_000004.10:15489361:G:T	NC_000004.12:15878640:G:T	(self)
19951368, 11110476, 7854857, 6597721, 4889380, 11637840, 170320, 4177847, 5090028, 10328286, 2723954, 22357526, 11110476, 2428159, ss331462771, ss557337593, ss651102337, ss979809627, ss1071307089, ss1308598106, ss1429787424, ss1580432782, ss1609495460, ss1652489493, ss1711054560, ss1801060932, ss1923048098, ss1969668873, ss2022097125, ss2150207600, ss2625549584, ss2705651813, ss2806099344, ss2994208831, ss3345565369, ss3662116609, ss3730892982, ss3761449822, ss3784630828, ss3790099944, ss3794974997, ss3828391442, ss3837629262, ss3858311306, ss3904460446, ss5164388219, ss5634434729, ss5843609325, ss5962812369	NC_000004.11:15880263:G:T	NC_000004.12:15878640:G:T	(self)
26228089, 141420444, 31926768, 441621279, 10726194396, ss2260737615, ss3024817721, ss3647661883, ss3711488232, ss3804583598, ss3843063449, ss4604243723, ss5258191522, ss5457074639, ss5538702154, ss5698089664, ss5804795004, ss5862311525	NC_000004.12:15878640:G:T	NC_000004.12:15878640:G:T	(self)
ss11647000, ss15686720, ss19565685, ss22112893	NT_006316.15:6555621:G:T	NC_000004.12:15878640:G:T	(self)
ss3549650, ss6471365, ss98805143	NT_006316.16:7062060:G:T	NC_000004.12:15878640: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 rs2532086

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

rs2532086