Name: rs9682063
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.

rs9682063

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr3:4696158 (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: A>C / A>G / A>T
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.352038 (93181/264690, TOPMED)
G=0.07456 (2107/28258, 14KJPN)
G=0.42579 (11946/28056, ALFA) (+ 12 more)
G=0.07399 (1240/16760, 8.3KJPN)
G=0.2275 (1457/6404, 1000G_30x)
G=0.2218 (1111/5008, 1000G)
G=0.4984 (2233/4480, Estonian)
G=0.0778 (228/2930, KOREAN)
A=0.429 (428/998, GoNL)
A=0.480 (288/600, NorthernSweden)
A=0.366 (90/246, SGDP_PRJ)
G=0.301 (65/216, Qatari)
G=0.121 (26/214, Vietnamese)
A=0.42 (17/40, GENOME_DK)
A=0.29 (10/34, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ITPR1 : Intron Variant
Publications: 1 citation
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	28056	A=0.57421	C=0.00000, G=0.42579, T=0.00000
European	Sub	24490	A=0.52103	C=0.00000, G=0.47897, T=0.00000
African	Sub	2372	A=0.9911	C=0.0000, G=0.0089, T=0.0000
African Others	Sub	110	A=1.000	C=0.000, G=0.000, T=0.000
African American	Sub	2262	A=0.9907	C=0.0000, G=0.0093, T=0.0000
Asian	Sub	140	A=0.964	C=0.000, G=0.036, T=0.000
East Asian	Sub	118	A=0.958	C=0.000, G=0.042, T=0.000
Other Asian	Sub	22	A=1.00	C=0.00, G=0.00, T=0.00
Latin American 1	Sub	70	A=1.00	C=0.00, G=0.00, T=0.00
Latin American 2	Sub	232	A=1.000	C=0.000, G=0.000, T=0.000
South Asian	Sub	64	A=0.98	C=0.00, G=0.02, T=0.00
Other	Sub	688	A=0.725	C=0.000, G=0.275, T=0.000

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	A=0.647962	G=0.352038
14KJPN	JAPANESE	Study-wide	28258	A=0.92544	G=0.07456
Allele Frequency Aggregator	Total	Global	28056	A=0.57421	C=0.00000, G=0.42579, T=0.00000
Allele Frequency Aggregator	European	Sub	24490	A=0.52103	C=0.00000, G=0.47897, T=0.00000
Allele Frequency Aggregator	African	Sub	2372	A=0.9911	C=0.0000, G=0.0089, T=0.0000
Allele Frequency Aggregator	Other	Sub	688	A=0.725	C=0.000, G=0.275, T=0.000
Allele Frequency Aggregator	Latin American 2	Sub	232	A=1.000	C=0.000, G=0.000, T=0.000
Allele Frequency Aggregator	Asian	Sub	140	A=0.964	C=0.000, G=0.036, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	70	A=1.00	C=0.00, G=0.00, T=0.00
Allele Frequency Aggregator	South Asian	Sub	64	A=0.98	C=0.00, G=0.02, T=0.00
8.3KJPN	JAPANESE	Study-wide	16760	A=0.92601	G=0.07399
1000Genomes_30x	Global	Study-wide	6404	A=0.7723	G=0.2275, T=0.0002
1000Genomes_30x	African	Sub	1786	A=0.9490	G=0.0510, T=0.0000
1000Genomes_30x	Europe	Sub	1266	A=0.5008	G=0.4984, T=0.0008
1000Genomes_30x	South Asian	Sub	1202	A=0.7820	G=0.2180, T=0.0000
1000Genomes_30x	East Asian	Sub	1170	A=0.9179	G=0.0821, T=0.0000
1000Genomes_30x	American	Sub	980	A=0.615	G=0.385, T=0.000
1000Genomes	Global	Study-wide	5008	A=0.7782	G=0.2218
1000Genomes	African	Sub	1322	A=0.9448	G=0.0552
1000Genomes	East Asian	Sub	1008	A=0.9187	G=0.0813
1000Genomes	Europe	Sub	1006	A=0.5149	G=0.4851
1000Genomes	South Asian	Sub	978	A=0.789	G=0.211
1000Genomes	American	Sub	694	A=0.622	G=0.378
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.5016	G=0.4984
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.9222	G=0.0778
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.429	G=0.571
Northern Sweden	ACPOP	Study-wide	600	A=0.480	G=0.520
SGDP_PRJ	Global	Study-wide	246	A=0.366	G=0.634
Qatari	Global	Study-wide	216	A=0.699	G=0.301
A Vietnamese Genetic Variation Database	Global	Study-wide	214	A=0.879	G=0.121
The Danish reference pan genome	Danish	Study-wide	40	A=0.42	G=0.57
Siberian	Global	Study-wide	34	A=0.29	G=0.71

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 3	NC_000003.12:g.4696158A>C
GRCh38.p14 chr 3	NC_000003.12:g.4696158A>G
GRCh38.p14 chr 3	NC_000003.12:g.4696158A>T
GRCh37.p13 chr 3	NC_000003.11:g.4737842A>C
GRCh37.p13 chr 3	NC_000003.11:g.4737842A>G
GRCh37.p13 chr 3	NC_000003.11:g.4737842A>T
ITPR1 RefSeqGene	NG_016144.1:g.207811A>C
ITPR1 RefSeqGene	NG_016144.1:g.207811A>G
ITPR1 RefSeqGene	NG_016144.1:g.207811A>T

Gene: ITPR1, inositol 1,4,5-trisphosphate receptor type 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ITPR1 transcript variant 1	NM_001099952.4:c.4255-989… NM_001099952.4:c.4255-989A>C	N/A	Intron Variant
ITPR1 transcript variant 3	NM_001168272.2:c.4237-989… NM_001168272.2:c.4237-989A>C	N/A	Intron Variant
ITPR1 transcript variant 4	NM_001378452.1:c.4282-989… NM_001378452.1:c.4282-989A>C	N/A	Intron Variant
ITPR1 transcript variant 2	NM_002222.7:c.4210-989A>C	N/A	Intron Variant

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	A=	C	G	T
GRCh38.p14 chr 3	NC_000003.12:g.4696158=	NC_000003.12:g.4696158A>C	NC_000003.12:g.4696158A>G	NC_000003.12:g.4696158A>T
GRCh37.p13 chr 3	NC_000003.11:g.4737842=	NC_000003.11:g.4737842A>C	NC_000003.11:g.4737842A>G	NC_000003.11:g.4737842A>T
ITPR1 RefSeqGene	NG_016144.1:g.207811=	NG_016144.1:g.207811A>C	NG_016144.1:g.207811A>G	NG_016144.1:g.207811A>T
ITPR1 transcript variant 1	NM_001099952.2:c.4255-989=	NM_001099952.2:c.4255-989A>C	NM_001099952.2:c.4255-989A>G	NM_001099952.2:c.4255-989A>T
ITPR1 transcript variant 1	NM_001099952.4:c.4255-989=	NM_001099952.4:c.4255-989A>C	NM_001099952.4:c.4255-989A>G	NM_001099952.4:c.4255-989A>T
ITPR1 transcript variant 3	NM_001168272.1:c.4237-989=	NM_001168272.1:c.4237-989A>C	NM_001168272.1:c.4237-989A>G	NM_001168272.1:c.4237-989A>T
ITPR1 transcript variant 3	NM_001168272.2:c.4237-989=	NM_001168272.2:c.4237-989A>C	NM_001168272.2:c.4237-989A>G	NM_001168272.2:c.4237-989A>T
ITPR1 transcript variant 4	NM_001378452.1:c.4282-989=	NM_001378452.1:c.4282-989A>C	NM_001378452.1:c.4282-989A>G	NM_001378452.1:c.4282-989A>T
ITPR1 transcript variant 2	NM_002222.5:c.4210-989=	NM_002222.5:c.4210-989A>C	NM_002222.5:c.4210-989A>G	NM_002222.5:c.4210-989A>T
ITPR1 transcript variant 2	NM_002222.7:c.4210-989=	NM_002222.7:c.4210-989A>C	NM_002222.7:c.4210-989A>G	NM_002222.7:c.4210-989A>T
ITPR1 transcript variant X1	XM_005265108.1:c.4282-989=	XM_005265108.1:c.4282-989A>C	XM_005265108.1:c.4282-989A>G	XM_005265108.1:c.4282-989A>T
ITPR1 transcript variant X2	XM_005265109.1:c.4282-989=	XM_005265109.1:c.4282-989A>C	XM_005265109.1:c.4282-989A>G	XM_005265109.1:c.4282-989A>T
ITPR1 transcript variant X3	XM_005265110.1:c.4282-989=	XM_005265110.1:c.4282-989A>C	XM_005265110.1:c.4282-989A>G	XM_005265110.1:c.4282-989A>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#.

60 SubSNP, 22 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WI_SSAHASNP	ss13481212	Dec 05, 2003 (119)
2	SC_SNP	ss14761112	Dec 05, 2003 (123)
3	BCMHGSC_JDW	ss91977761	Mar 24, 2008 (129)
4	HUMANGENOME_JCVI	ss95980403	Feb 05, 2009 (130)
5	1000GENOMES	ss111158359	Jan 25, 2009 (130)
6	ENSEMBL	ss138691265	Dec 01, 2009 (131)
7	ENSEMBL	ss143427010	Dec 01, 2009 (131)
8	COMPLETE_GENOMICS	ss161901398	Jul 04, 2010 (132)
9	BCM-HGSC-SUB	ss206006741	Jul 04, 2010 (132)
10	1000GENOMES	ss231684484	Jul 14, 2010 (132)
11	GMI	ss276990817	May 04, 2012 (137)
12	GMI	ss284583746	Apr 25, 2013 (138)
13	PJP	ss292786177	May 09, 2011 (134)
14	SSMP	ss650050599	Apr 25, 2013 (138)
15	EVA-GONL	ss978212425	Aug 21, 2014 (142)
16	JMKIDD_LAB	ss1070129332	Aug 21, 2014 (142)
17	1000GENOMES	ss1302582606	Aug 21, 2014 (142)
18	EVA_GENOME_DK	ss1579820809	Apr 01, 2015 (144)
19	EVA_DECODE	ss1587672234	Apr 01, 2015 (144)
20	EVA_UK10K_ALSPAC	ss1606296663	Apr 01, 2015 (144)
21	EVA_UK10K_ALSPAC	ss1606296664	Apr 01, 2015 (144)
22	EVA_UK10K_TWINSUK	ss1649290696	Apr 01, 2015 (144)
23	EVA_UK10K_TWINSUK	ss1649290697	Apr 01, 2015 (144)
24	WEILL_CORNELL_DGM	ss1921464688	Feb 12, 2016 (147)
25	GENOMED	ss1969308665	Jul 19, 2016 (147)
26	JJLAB	ss2021283325	Sep 14, 2016 (149)
27	USC_VALOUEV	ss2149350797	Dec 20, 2016 (150)
28	HUMAN_LONGEVITY	ss2248639876	Dec 20, 2016 (150)
29	SYSTEMSBIOZJU	ss2625141553	Nov 08, 2017 (151)
30	GRF	ss2704707736	Nov 08, 2017 (151)
31	ILLUMINA	ss2710963464	Nov 08, 2017 (151)
32	GNOMAD	ss2788933611	Nov 08, 2017 (151)
33	SWEGEN	ss2991742439	Nov 08, 2017 (151)
34	CSHL	ss3344857313	Nov 08, 2017 (151)
35	BIOINF_KMB_FNS_UNIBA	ss3645693657	Oct 11, 2018 (152)
36	URBANLAB	ss3647328736	Oct 11, 2018 (152)
37	EGCUT_WGS	ss3659639840	Jul 13, 2019 (153)
38	EVA_DECODE	ss3708529701	Jul 13, 2019 (153)
39	ACPOP	ss3729583508	Jul 13, 2019 (153)
40	EVA	ss3759590940	Jul 13, 2019 (153)
41	KHV_HUMAN_GENOMES	ss3802741988	Jul 13, 2019 (153)
42	EVA	ss3827632069	Apr 25, 2020 (154)
43	EVA	ss3837237353	Apr 25, 2020 (154)
44	EVA	ss3842660908	Apr 25, 2020 (154)
45	SGDP_PRJ	ss3855108339	Apr 25, 2020 (154)
46	KRGDB	ss3900874040	Apr 25, 2020 (154)
47	TOPMED	ss4552422632	Apr 27, 2021 (155)
48	TOMMO_GENOMICS	ss5157558489	Apr 27, 2021 (155)
49	1000G_HIGH_COVERAGE	ss5252857392	Oct 13, 2022 (156)
50	EVA	ss5337540379	Oct 13, 2022 (156)
51	HUGCELL_USP	ss5452380429	Oct 13, 2022 (156)
52	HUGCELL_USP	ss5452380430	Oct 13, 2022 (156)
53	1000G_HIGH_COVERAGE	ss5530596559	Oct 13, 2022 (156)
54	SANFORD_IMAGENETICS	ss5631430665	Oct 13, 2022 (156)
55	TOMMO_GENOMICS	ss5688758676	Oct 13, 2022 (156)
56	YY_MCH	ss5803432003	Oct 13, 2022 (156)
57	EVA	ss5825270794	Oct 13, 2022 (156)
58	EVA	ss5853465257	Oct 13, 2022 (156)
59	EVA	ss5867410665	Oct 13, 2022 (156)
60	EVA	ss5959687092	Oct 13, 2022 (156)
61	1000Genomes	NC_000003.11 - 4737842	Oct 11, 2018 (152)
62	1000Genomes_30x	NC_000003.12 - 4696158	Oct 13, 2022 (156)
63	The Avon Longitudinal Study of Parents and Children Submission ignored due to conflicting rows: Row 7603297 (NC_000003.11:4737841:A:A 1737/3854, NC_000003.11:4737841:A:G 2117/3854) Row 7603298 (NC_000003.11:4737841:A:A 3853/3854, NC_000003.11:4737841:A:T 1/3854)	-	Oct 11, 2018 (152)
64	The Avon Longitudinal Study of Parents and Children Submission ignored due to conflicting rows: Row 7603297 (NC_000003.11:4737841:A:A 1737/3854, NC_000003.11:4737841:A:G 2117/3854) Row 7603298 (NC_000003.11:4737841:A:A 3853/3854, NC_000003.11:4737841:A:T 1/3854)	-	Oct 11, 2018 (152)
65	Genetic variation in the Estonian population	NC_000003.11 - 4737842	Oct 11, 2018 (152)
66	The Danish reference pan genome	NC_000003.11 - 4737842	Apr 25, 2020 (154)
67	gnomAD - Genomes Submission ignored due to conflicting rows: Row 97522212 (NC_000003.12:4696157:A:C 1/140100) Row 97522213 (NC_000003.12:4696157:A:G 52484/140054) Row 97522214 (NC_000003.12:4696157:A:T 5/140100)	-	Apr 27, 2021 (155)
68	gnomAD - Genomes Submission ignored due to conflicting rows: Row 97522212 (NC_000003.12:4696157:A:C 1/140100) Row 97522213 (NC_000003.12:4696157:A:G 52484/140054) Row 97522214 (NC_000003.12:4696157:A:T 5/140100)	-	Apr 27, 2021 (155)
69	gnomAD - Genomes Submission ignored due to conflicting rows: Row 97522212 (NC_000003.12:4696157:A:C 1/140100) Row 97522213 (NC_000003.12:4696157:A:G 52484/140054) Row 97522214 (NC_000003.12:4696157:A:T 5/140100)	-	Apr 27, 2021 (155)
70	Genome of the Netherlands Release 5	NC_000003.11 - 4737842	Apr 25, 2020 (154)
71	KOREAN population from KRGDB	NC_000003.11 - 4737842	Apr 25, 2020 (154)
72	Northern Sweden	NC_000003.11 - 4737842	Jul 13, 2019 (153)
73	Qatari	NC_000003.11 - 4737842	Apr 25, 2020 (154)
74	SGDP_PRJ	NC_000003.11 - 4737842	Apr 25, 2020 (154)
75	Siberian	NC_000003.11 - 4737842	Apr 25, 2020 (154)
76	8.3KJPN	NC_000003.11 - 4737842	Apr 27, 2021 (155)
77	14KJPN	NC_000003.12 - 4696158	Oct 13, 2022 (156)
78	TopMed	NC_000003.12 - 4696158	Apr 27, 2021 (155)
79	UK 10K study - Twins Submission ignored due to conflicting rows: Row 7603297 (NC_000003.11:4737841:A:A 1676/3708, NC_000003.11:4737841:A:G 2032/3708) Row 7603298 (NC_000003.11:4737841:A:A 3708/3708, NC_000003.11:4737841:A:T 0/3708)	-	Oct 11, 2018 (152)
80	UK 10K study - Twins Submission ignored due to conflicting rows: Row 7603297 (NC_000003.11:4737841:A:A 1676/3708, NC_000003.11:4737841:A:G 2032/3708) Row 7603298 (NC_000003.11:4737841:A:A 3708/3708, NC_000003.11:4737841:A:T 0/3708)	-	Oct 11, 2018 (152)
81	A Vietnamese Genetic Variation Database	NC_000003.11 - 4737842	Jul 13, 2019 (153)
82	ALFA	NC_000003.12 - 4696158	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)
rs10440147	Sep 24, 2004 (123)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
3623558073	NC_000003.12:4696157:A:C	NC_000003.12:4696157:A:C	(self)
ss91977761, ss111158359, ss161901398, ss206006741, ss276990817, ss284583746, ss292786177, ss1587672234	NC_000003.10:4712841:A:G	NC_000003.12:4696157:A:G	(self)
13720362, 5378088, 5985748, 3336633, 8051434, 2868373, 3506618, 7125319, 1867151, 15527796, 1654320, ss231684484, ss650050599, ss978212425, ss1070129332, ss1302582606, ss1579820809, ss1606296663, ss1649290696, ss1921464688, ss1969308665, ss2021283325, ss2149350797, ss2625141553, ss2704707736, ss2710963464, ss2788933611, ss2991742439, ss3344857313, ss3659639840, ss3729583508, ss3759590940, ss3827632069, ss3837237353, ss3855108339, ss3900874040, ss5157558489, ss5337540379, ss5631430665, ss5825270794, ss5959687092	NC_000003.11:4737841:A:G	NC_000003.12:4696157:A:G	(self)
18122494, 22595780, 389800187, 3623558073, ss2248639876, ss3645693657, ss3647328736, ss3708529701, ss3802741988, ss3842660908, ss4552422632, ss5252857392, ss5452380429, ss5530596559, ss5688758676, ss5803432003, ss5853465257, ss5867410665	NC_000003.12:4696157:A:G	NC_000003.12:4696157:A:G	(self)
ss13481212, ss14761112	NT_022517.16:4677841:A:G	NC_000003.12:4696157:A:G	(self)
ss95980403, ss138691265, ss143427010	NT_022517.18:4677841:A:G	NC_000003.12:4696157:A:G	(self)
ss1606296664, ss1649290697, ss2788933611	NC_000003.11:4737841:A:T	NC_000003.12:4696157:A:T	(self)
18122494, 3623558073, ss2248639876, ss5452380430, ss5530596559	NC_000003.12:4696157:A:T	NC_000003.12:4696157:A:T	(self)

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

1 citation for rs9682063

PMID	Title	Author	Year	Journal
28235418	BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes.	de Santiago I et al.	2017	Genome biology

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

rs9682063