Name: rs2562132
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.

rs2562132

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr16:34170 (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: C>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.496154 (131327/264690, TOPMED)
C=0.486550 (68079/139922, GnomAD)
C=0.43446 (12276/28256, 14KJPN) (+ 17 more)
C=0.42832 (8091/18890, ALFA)
C=0.43591 (7305/16758, 8.3KJPN)
T=0.4710 (3016/6404, 1000G_30x)
T=0.4792 (2400/5008, 1000G)
C=0.3983 (1535/3854, ALSPAC)
C=0.3937 (1460/3708, TWINSUK)
C=0.4536 (1329/2930, KOREAN)
C=0.4329 (793/1832, Korea1K)
C=0.407 (406/998, GoNL)
C=0.377 (226/600, NorthernSweden)
T=0.418 (223/534, MGP)
C=0.327 (136/416, SGDP_PRJ)
T=0.439 (143/326, HapMap)
T=0.458 (99/216, Qatari)
C=0.454 (98/216, Vietnamese)
T=0.31 (22/70, Ancient Sardinia)
C=0.20 (10/50, 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	C=0.42832	T=0.57168
European	Sub	14286	C=0.37337	T=0.62663
African	Sub	2946	C=0.6704	T=0.3296
African Others	Sub	114	C=0.658	T=0.342
African American	Sub	2832	C=0.6709	T=0.3291
Asian	Sub	112	C=0.357	T=0.643
East Asian	Sub	86	C=0.42	T=0.58
Other Asian	Sub	26	C=0.15	T=0.85
Latin American 1	Sub	146	C=0.582	T=0.418
Latin American 2	Sub	610	C=0.439	T=0.561
South Asian	Sub	98	C=0.35	T=0.65
Other	Sub	692	C=0.513	T=0.487

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	C=0.503846	T=0.496154
gnomAD - Genomes	Global	Study-wide	139922	C=0.486550	T=0.513450
gnomAD - Genomes	European	Sub	75814	C=0.38861	T=0.61139
gnomAD - Genomes	African	Sub	41880	C=0.66810	T=0.33190
gnomAD - Genomes	American	Sub	13636	C=0.49795	T=0.50205
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	C=0.4497	T=0.5503
gnomAD - Genomes	East Asian	Sub	3120	C=0.4035	T=0.5965
gnomAD - Genomes	Other	Sub	2152	C=0.5088	T=0.4912
14KJPN	JAPANESE	Study-wide	28256	C=0.43446	T=0.56554
Allele Frequency Aggregator	Total	Global	18890	C=0.42832	T=0.57168
Allele Frequency Aggregator	European	Sub	14286	C=0.37337	T=0.62663
Allele Frequency Aggregator	African	Sub	2946	C=0.6704	T=0.3296
Allele Frequency Aggregator	Other	Sub	692	C=0.513	T=0.487
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.439	T=0.561
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.582	T=0.418
Allele Frequency Aggregator	Asian	Sub	112	C=0.357	T=0.643
Allele Frequency Aggregator	South Asian	Sub	98	C=0.35	T=0.65
8.3KJPN	JAPANESE	Study-wide	16758	C=0.43591	T=0.56409
1000Genomes_30x	Global	Study-wide	6404	C=0.5290	T=0.4710
1000Genomes_30x	African	Sub	1786	C=0.7301	T=0.2699
1000Genomes_30x	Europe	Sub	1266	C=0.4155	T=0.5845
1000Genomes_30x	South Asian	Sub	1202	C=0.4742	T=0.5258
1000Genomes_30x	East Asian	Sub	1170	C=0.4077	T=0.5923
1000Genomes_30x	American	Sub	980	C=0.521	T=0.479
1000Genomes	Global	Study-wide	5008	C=0.5208	T=0.4792
1000Genomes	African	Sub	1322	C=0.7345	T=0.2655
1000Genomes	East Asian	Sub	1008	C=0.4008	T=0.5992
1000Genomes	Europe	Sub	1006	C=0.4056	T=0.5944
1000Genomes	South Asian	Sub	978	C=0.473	T=0.527
1000Genomes	American	Sub	694	C=0.522	T=0.478
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.3983	T=0.6017
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.3937	T=0.6063
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.4536	G=0.0000, T=0.5464
Korean Genome Project	KOREAN	Study-wide	1832	C=0.4329	T=0.5671
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.407	T=0.593
Northern Sweden	ACPOP	Study-wide	600	C=0.377	T=0.623
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	C=0.582	T=0.418
SGDP_PRJ	Global	Study-wide	416	C=0.327	T=0.673
HapMap	Global	Study-wide	326	C=0.561	T=0.439
HapMap	African	Sub	120	C=0.750	T=0.250
HapMap	American	Sub	118	C=0.407	T=0.593
HapMap	Asian	Sub	88	C=0.51	T=0.49
Qatari	Global	Study-wide	216	C=0.542	T=0.458
A Vietnamese Genetic Variation Database	Global	Study-wide	216	C=0.454	T=0.546
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	70	C=0.69	T=0.31
Siberian	Global	Study-wide	50	C=0.20	T=0.80

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 16	NC_000016.10:g.34170C>G
GRCh38.p14 chr 16	NC_000016.10:g.34170C>T
GRCh37.p13 chr 16	NC_000016.9:g.84170C>G
GRCh37.p13 chr 16	NC_000016.9:g.84170C>T
IL9RP3 pseudogene	NG_009865.1:g.2422G>C
IL9RP3 pseudogene	NG_009865.1:g.2422G>A

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	C=	G	T
GRCh38.p14 chr 16	NC_000016.10:g.34170=	NC_000016.10:g.34170C>G	NC_000016.10:g.34170C>T
GRCh37.p13 chr 16	NC_000016.9:g.84170=	NC_000016.9:g.84170C>G	NC_000016.9:g.84170C>T
IL9RP3 pseudogene	NG_009865.1:g.2422=	NG_009865.1:g.2422G>C	NG_009865.1:g.2422G>A

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#.

76 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss3596652	Sep 28, 2001 (100)
2	YUSUKE	ss4929880	Aug 28, 2002 (108)
3	CSHL-HAPMAP	ss17563601	Feb 27, 2004 (120)
4	SSAHASNP	ss21372455	Apr 05, 2004 (121)
5	PERLEGEN	ss24398579	Sep 20, 2004 (123)
6	ABI	ss40708069	Mar 13, 2006 (126)
7	HGSV	ss78502905	Dec 06, 2007 (129)
8	HUMANGENOME_JCVI	ss96616636	Feb 05, 2009 (130)
9	BGI	ss103270620	Dec 01, 2009 (131)
10	1000GENOMES	ss109110411	Jan 23, 2009 (130)
11	ENSEMBL	ss136771759	Dec 01, 2009 (131)
12	GMI	ss156963256	Dec 01, 2009 (131)
13	COMPLETE_GENOMICS	ss167616300	Jul 04, 2010 (132)
14	COMPLETE_GENOMICS	ss170817822	Jul 04, 2010 (132)
15	BUSHMAN	ss201298510	Jul 04, 2010 (132)
16	BCM-HGSC-SUB	ss207650441	Jul 04, 2010 (132)
17	1000GENOMES	ss211667546	Jul 14, 2010 (132)
18	1000GENOMES	ss227085759	Jul 14, 2010 (132)
19	1000GENOMES	ss236913538	Jul 15, 2010 (132)
20	1000GENOMES	ss243275698	Jul 15, 2010 (132)
21	GMI	ss282398978	May 04, 2012 (137)
22	GMI	ss287016993	Apr 25, 2013 (138)
23	PJP	ss291831154	May 09, 2011 (134)
24	TISHKOFF	ss564709975	Apr 25, 2013 (138)
25	SSMP	ss660454656	Apr 25, 2013 (138)
26	EVA-GONL	ss992173190	Aug 21, 2014 (142)
27	JMKIDD_LAB	ss1080408235	Aug 21, 2014 (142)
28	1000GENOMES	ss1354950681	Aug 21, 2014 (142)
29	DDI	ss1427745385	Apr 01, 2015 (144)
30	EVA_UK10K_ALSPAC	ss1633790662	Apr 01, 2015 (144)
31	EVA_UK10K_TWINSUK	ss1676784695	Apr 01, 2015 (144)
32	EVA_DECODE	ss1696205746	Apr 01, 2015 (144)
33	EVA_MGP	ss1711412558	Apr 01, 2015 (144)
34	HAMMER_LAB	ss1808371003	Sep 08, 2015 (146)
35	WEILL_CORNELL_DGM	ss1935578229	Feb 12, 2016 (147)
36	ILLUMINA	ss1959646288	Feb 12, 2016 (147)
37	GENOMED	ss1968196460	Jul 19, 2016 (147)
38	JJLAB	ss2028576399	Sep 14, 2016 (149)
39	USC_VALOUEV	ss2156983722	Nov 08, 2017 (151)
40	SYSTEMSBIOZJU	ss2628782710	Nov 08, 2017 (151)
41	GRF	ss2701477510	Nov 08, 2017 (151)
42	GNOMAD	ss2939122571	Nov 08, 2017 (151)
43	SWEGEN	ss3013892020	Nov 08, 2017 (151)
44	ILLUMINA	ss3021670290	Nov 08, 2017 (151)
45	BIOINF_KMB_FNS_UNIBA	ss3028112955	Nov 08, 2017 (151)
46	CSHL	ss3351285311	Nov 08, 2017 (151)
47	OMUKHERJEE_ADBS	ss3646482959	Oct 12, 2018 (152)
48	URBANLAB	ss3650440421	Oct 12, 2018 (152)
49	ILLUMINA	ss3652073824	Oct 12, 2018 (152)
50	EVA_DECODE	ss3698629027	Jul 13, 2019 (153)
51	ACPOP	ss3741245839	Jul 13, 2019 (153)
52	EVA	ss3753552184	Jul 13, 2019 (153)
53	PACBIO	ss3787952272	Jul 13, 2019 (153)
54	PACBIO	ss3792948346	Jul 13, 2019 (153)
55	PACBIO	ss3797833087	Jul 13, 2019 (153)
56	KHV_HUMAN_GENOMES	ss3818854411	Jul 13, 2019 (153)
57	EVA	ss3834421791	Apr 27, 2020 (154)
58	EVA	ss3840815464	Apr 27, 2020 (154)
59	SGDP_PRJ	ss3883708413	Apr 27, 2020 (154)
60	KRGDB	ss3932973609	Apr 27, 2020 (154)
61	KOGIC	ss3976907229	Apr 27, 2020 (154)
62	EVA	ss3985740354	Apr 26, 2021 (155)
63	TOPMED	ss5004235164	Apr 26, 2021 (155)
64	TOMMO_GENOMICS	ss5217926519	Apr 26, 2021 (155)
65	1000G_HIGH_COVERAGE	ss5299753302	Oct 16, 2022 (156)
66	EVA	ss5421630317	Oct 16, 2022 (156)
67	HUGCELL_USP	ss5493330778	Oct 16, 2022 (156)
68	1000G_HIGH_COVERAGE	ss5601804818	Oct 16, 2022 (156)
69	SANFORD_IMAGENETICS	ss5658253034	Oct 16, 2022 (156)
70	TOMMO_GENOMICS	ss5772250206	Oct 16, 2022 (156)
71	YY_MCH	ss5815665281	Oct 16, 2022 (156)
72	EVA	ss5845956103	Oct 16, 2022 (156)
73	EVA	ss5851447622	Oct 16, 2022 (156)
74	EVA	ss5897860568	Oct 16, 2022 (156)
75	EVA	ss5949680305	Oct 16, 2022 (156)
76	EVA	ss5980895617	Oct 16, 2022 (156)
77	1000Genomes	NC_000016.9 - 84170	Oct 12, 2018 (152)
78	1000Genomes_30x	NC_000016.10 - 34170	Oct 16, 2022 (156)
79	The Avon Longitudinal Study of Parents and Children	NC_000016.9 - 84170	Oct 12, 2018 (152)
80	gnomAD - Genomes	NC_000016.10 - 34170	Apr 26, 2021 (155)
81	Genome of the Netherlands Release 5	NC_000016.9 - 84170	Apr 27, 2020 (154)
82	HapMap	NC_000016.10 - 34170	Apr 27, 2020 (154)
83	KOREAN population from KRGDB	NC_000016.9 - 84170	Apr 27, 2020 (154)
84	Korean Genome Project	NC_000016.10 - 34170	Apr 27, 2020 (154)
85	Medical Genome Project healthy controls from Spanish population	NC_000016.9 - 84170	Apr 27, 2020 (154)
86	Northern Sweden	NC_000016.9 - 84170	Jul 13, 2019 (153)
87	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000016.9 - 84170	Apr 26, 2021 (155)
88	Qatari	NC_000016.9 - 84170	Apr 27, 2020 (154)
89	SGDP_PRJ	NC_000016.9 - 84170	Apr 27, 2020 (154)
90	Siberian	NC_000016.9 - 84170	Apr 27, 2020 (154)
91	8.3KJPN	NC_000016.9 - 84170	Apr 26, 2021 (155)
92	14KJPN	NC_000016.10 - 34170	Oct 16, 2022 (156)
93	TopMed	NC_000016.10 - 34170	Apr 26, 2021 (155)
94	UK 10K study - Twins	NC_000016.9 - 84170	Oct 12, 2018 (152)
95	A Vietnamese Genetic Variation Database	NC_000016.9 - 84170	Jul 13, 2019 (153)
96	ALFA	NC_000016.10 - 34170	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)
rs3743873	Oct 09, 2002 (108)
rs17797163	Oct 08, 2004 (123)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
40151003, ss3932973609	NC_000016.9:84169:C:G	NC_000016.10:34169:C:G	(self)
ss78502905, ss109110411, ss167616300, ss170817822, ss201298510, ss207650441, ss211667546, ss282398978, ss287016993, ss291831154, ss1696205746	NC_000016.8:24169:C:T	NC_000016.10:34169:C:T	(self)
68075260, 37807972, 16869798, 40151003, 528318, 14530704, 966281, 17620151, 35725393, 9500076, 75895826, 37807972, 8405286, ss227085759, ss236913538, ss243275698, ss564709975, ss660454656, ss992173190, ss1080408235, ss1354950681, ss1427745385, ss1633790662, ss1676784695, ss1711412558, ss1808371003, ss1935578229, ss1959646288, ss1968196460, ss2028576399, ss2156983722, ss2628782710, ss2701477510, ss2939122571, ss3013892020, ss3021670290, ss3351285311, ss3646482959, ss3652073824, ss3741245839, ss3753552184, ss3787952272, ss3792948346, ss3797833087, ss3834421791, ss3840815464, ss3883708413, ss3932973609, ss3985740354, ss5217926519, ss5421630317, ss5658253034, ss5845956103, ss5949680305, ss5980895617	NC_000016.9:84169:C:T	NC_000016.10:34169:C:T	(self)
89330753, 479811947, 1332233, 33285230, 106087310, 219780825, 96231281, ss3028112955, ss3650440421, ss3698629027, ss3818854411, ss3976907229, ss5004235164, ss5299753302, ss5493330778, ss5601804818, ss5772250206, ss5815665281, ss5851447622, ss5897860568	NC_000016.10:34169:C:T	NC_000016.10:34169:C:T	(self)
ss3596652, ss4929880, ss24398579, ss40708069, ss96616636, ss103270620, ss136771759, ss156963256	NT_010393.16:24169:C:T	NC_000016.10:34169:C:T	(self)
ss17563601, ss21372455	NT_037887.3:24169:C:T	NC_000016.10:34169:C: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 rs2562132

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

rs2562132