Name: rs1002589
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.

rs1002589

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr10:44631439 (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: C=0.454513 (120305/264690, TOPMED)
C=0.463291 (68531/147922, ALFA)
C=0.449306 (62866/139918, GnomAD) (+ 18 more)
C=0.22825 (6450/28258, 14KJPN)
C=0.22768 (3816/16760, 8.3KJPN)
C=0.4277 (2739/6404, 1000G_30x)
C=0.4251 (2129/5008, 1000G)
C=0.4638 (2078/4480, Estonian)
C=0.4779 (1842/3854, ALSPAC)
C=0.4587 (1701/3708, TWINSUK)
C=0.1853 (543/2930, KOREAN)
C=0.1949 (357/1832, Korea1K)
C=0.3945 (707/1792, HapMap)
C=0.468 (467/998, GoNL)
C=0.447 (280/626, Chileans)
C=0.433 (260/600, NorthernSweden)
T=0.315 (117/372, SGDP_PRJ)
C=0.444 (96/216, Qatari)
C=0.319 (67/210, Vietnamese)
C=0.47 (19/40, GENOME_DK)
T=0.33 (4/12, 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	147922	T=0.536709	A=0.000000, C=0.463291
European	Sub	125444	T=0.538232	A=0.000000, C=0.461768
African	Sub	5810	T=0.5962	A=0.0000, C=0.4038
African Others	Sub	202	T=0.589	A=0.000, C=0.411
African American	Sub	5608	T=0.5965	A=0.0000, C=0.4035
Asian	Sub	666	T=0.728	A=0.000, C=0.272
East Asian	Sub	504	T=0.760	A=0.000, C=0.240
Other Asian	Sub	162	T=0.630	A=0.000, C=0.370
Latin American 1	Sub	874	T=0.491	A=0.000, C=0.509
Latin American 2	Sub	8410	T=0.4604	A=0.0000, C=0.5396
South Asian	Sub	196	T=0.561	A=0.000, C=0.439
Other	Sub	6522	T=0.5386	A=0.0000, C=0.4614

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=0.545487	C=0.454513
Allele Frequency Aggregator	Total	Global	147922	T=0.536709	A=0.000000, C=0.463291
Allele Frequency Aggregator	European	Sub	125444	T=0.538232	A=0.000000, C=0.461768
Allele Frequency Aggregator	Latin American 2	Sub	8410	T=0.4604	A=0.0000, C=0.5396
Allele Frequency Aggregator	Other	Sub	6522	T=0.5386	A=0.0000, C=0.4614
Allele Frequency Aggregator	African	Sub	5810	T=0.5962	A=0.0000, C=0.4038
Allele Frequency Aggregator	Latin American 1	Sub	874	T=0.491	A=0.000, C=0.509
Allele Frequency Aggregator	Asian	Sub	666	T=0.728	A=0.000, C=0.272
Allele Frequency Aggregator	South Asian	Sub	196	T=0.561	A=0.000, C=0.439
gnomAD - Genomes	Global	Study-wide	139918	T=0.550694	C=0.449306
gnomAD - Genomes	European	Sub	75802	T=0.53501	C=0.46499
gnomAD - Genomes	African	Sub	41892	T=0.57682	C=0.42318
gnomAD - Genomes	American	Sub	13630	T=0.50264	C=0.49736
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	T=0.5924	C=0.4076
gnomAD - Genomes	East Asian	Sub	3120	T=0.7349	C=0.2651
gnomAD - Genomes	Other	Sub	2152	T=0.5674	C=0.4326
14KJPN	JAPANESE	Study-wide	28258	T=0.77175	C=0.22825
8.3KJPN	JAPANESE	Study-wide	16760	T=0.77232	C=0.22768
1000Genomes_30x	Global	Study-wide	6404	T=0.5723	C=0.4277
1000Genomes_30x	African	Sub	1786	T=0.5890	C=0.4110
1000Genomes_30x	Europe	Sub	1266	T=0.5253	C=0.4747
1000Genomes_30x	South Asian	Sub	1202	T=0.5316	C=0.4684
1000Genomes_30x	East Asian	Sub	1170	T=0.7325	C=0.2675
1000Genomes_30x	American	Sub	980	T=0.461	C=0.539
1000Genomes	Global	Study-wide	5008	T=0.5749	C=0.4251
1000Genomes	African	Sub	1322	T=0.5825	C=0.4175
1000Genomes	East Asian	Sub	1008	T=0.7401	C=0.2599
1000Genomes	Europe	Sub	1006	T=0.5258	C=0.4742
1000Genomes	South Asian	Sub	978	T=0.520	C=0.480
1000Genomes	American	Sub	694	T=0.468	C=0.532
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.5362	C=0.4638
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.5221	C=0.4779
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.5413	C=0.4587
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.8147	C=0.1853
Korean Genome Project	KOREAN	Study-wide	1832	T=0.8051	C=0.1949
HapMap	Global	Study-wide	1792	T=0.6055	C=0.3945
HapMap	African	Sub	692	T=0.559	C=0.441
HapMap	American	Sub	670	T=0.599	C=0.401
HapMap	Asian	Sub	254	T=0.780	C=0.220
HapMap	Europe	Sub	176	T=0.562	C=0.438
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.532	C=0.468
Chileans	Chilean	Study-wide	626	T=0.553	C=0.447
Northern Sweden	ACPOP	Study-wide	600	T=0.567	C=0.433
SGDP_PRJ	Global	Study-wide	372	T=0.315	C=0.685
Qatari	Global	Study-wide	216	T=0.556	C=0.444
A Vietnamese Genetic Variation Database	Global	Study-wide	210	T=0.681	C=0.319
The Danish reference pan genome	Danish	Study-wide	40	T=0.53	C=0.47
Siberian	Global	Study-wide	12	T=0.33	C=0.67

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 10	NC_000010.11:g.44631439T>A
GRCh38.p14 chr 10	NC_000010.11:g.44631439T>C
GRCh37.p13 chr 10	NC_000010.10:g.45126887T>A
GRCh37.p13 chr 10	NC_000010.10:g.45126887T>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 10	NC_000010.11:g.44631439=	NC_000010.11:g.44631439T>A	NC_000010.11:g.44631439T>C
GRCh37.p13 chr 10	NC_000010.10:g.45126887=	NC_000010.10:g.45126887T>A	NC_000010.10:g.45126887T>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#.

106 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss1463401	Oct 05, 2000 (86)
2	SC_JCM	ss6149136	Feb 20, 2003 (111)
3	CSHL-HAPMAP	ss19171098	Feb 27, 2004 (120)
4	PERLEGEN	ss24550372	Sep 20, 2004 (123)
5	ABI	ss38603237	Mar 15, 2006 (126)
6	ILLUMINA	ss65714023	Oct 15, 2006 (127)
7	AFFY	ss66217052	Nov 30, 2006 (127)
8	CSHL-HAPMAP	ss68365900	Jan 12, 2007 (127)
9	AFFY	ss76363473	Dec 06, 2007 (129)
10	KRIBB_YJKIM	ss81449941	Dec 15, 2007 (130)
11	HUMANGENOME_JCVI	ss97644066	Feb 05, 2009 (130)
12	1000GENOMES	ss109397771	Jan 24, 2009 (130)
13	1000GENOMES	ss113180098	Jan 25, 2009 (130)
14	ENSEMBL	ss138678463	Dec 01, 2009 (131)
15	GMI	ss154947975	Dec 01, 2009 (131)
16	ILLUMINA	ss159853255	Dec 01, 2009 (131)
17	COMPLETE_GENOMICS	ss168268057	Jul 04, 2010 (132)
18	COMPLETE_GENOMICS	ss169789521	Jul 04, 2010 (132)
19	AFFY	ss173387213	Jul 04, 2010 (132)
20	COMPLETE_GENOMICS	ss174514730	Jul 04, 2010 (132)
21	BUSHMAN	ss201451573	Jul 04, 2010 (132)
22	BCM-HGSC-SUB	ss207170253	Jul 04, 2010 (132)
23	1000GENOMES	ss224695481	Jul 14, 2010 (132)
24	1000GENOMES	ss235153933	Jul 15, 2010 (132)
25	1000GENOMES	ss241864669	Jul 15, 2010 (132)
26	BL	ss254269888	May 09, 2011 (134)
27	GMI	ss280594354	May 04, 2012 (137)
28	PJP	ss291027461	May 09, 2011 (134)
29	ILLUMINA	ss479160740	May 04, 2012 (137)
30	ILLUMINA	ss479162515	May 04, 2012 (137)
31	ILLUMINA	ss479479600	Sep 08, 2015 (146)
32	ILLUMINA	ss484381538	May 04, 2012 (137)
33	ILLUMINA	ss536566895	Sep 08, 2015 (146)
34	TISHKOFF	ss561922451	Apr 25, 2013 (138)
35	SSMP	ss656644992	Apr 25, 2013 (138)
36	ILLUMINA	ss778344362	Sep 08, 2015 (146)
37	ILLUMINA	ss782637065	Sep 08, 2015 (146)
38	ILLUMINA	ss783606585	Sep 08, 2015 (146)
39	ILLUMINA	ss831887181	Sep 08, 2015 (146)
40	ILLUMINA	ss833799000	Sep 08, 2015 (146)
41	EVA-GONL	ss987436312	Aug 21, 2014 (142)
42	JMKIDD_LAB	ss1076946670	Aug 21, 2014 (142)
43	1000GENOMES	ss1337235231	Aug 21, 2014 (142)
44	DDI	ss1426301916	Apr 01, 2015 (144)
45	EVA_GENOME_DK	ss1575079872	Apr 01, 2015 (144)
46	EVA_DECODE	ss1597101342	Apr 01, 2015 (144)
47	EVA_UK10K_ALSPAC	ss1624472601	Apr 01, 2015 (144)
48	EVA_UK10K_TWINSUK	ss1667466634	Apr 01, 2015 (144)
49	EVA_SVP	ss1713175523	Apr 01, 2015 (144)
50	ILLUMINA	ss1751968998	Sep 08, 2015 (146)
51	HAMMER_LAB	ss1806364469	Sep 08, 2015 (146)
52	WEILL_CORNELL_DGM	ss1930786660	Feb 12, 2016 (147)
53	GENOMED	ss1967114423	Jul 19, 2016 (147)
54	JJLAB	ss2026117586	Sep 14, 2016 (149)
55	USC_VALOUEV	ss2154390511	Dec 20, 2016 (150)
56	HUMAN_LONGEVITY	ss2174409265	Dec 20, 2016 (150)
57	SYSTEMSBIOZJU	ss2627528145	Nov 08, 2017 (151)
58	ILLUMINA	ss2632705049	Nov 08, 2017 (151)
59	GRF	ss2698627035	Nov 08, 2017 (151)
60	GNOMAD	ss2888168869	Nov 08, 2017 (151)
61	SWEGEN	ss3006380255	Nov 08, 2017 (151)
62	BIOINF_KMB_FNS_UNIBA	ss3026847723	Nov 08, 2017 (151)
63	CSHL	ss3349092686	Nov 08, 2017 (151)
64	ILLUMINA	ss3626436363	Oct 12, 2018 (152)
65	ILLUMINA	ss3630731228	Oct 12, 2018 (152)
66	ILLUMINA	ss3632947493	Oct 12, 2018 (152)
67	ILLUMINA	ss3633644531	Oct 12, 2018 (152)
68	ILLUMINA	ss3634401087	Oct 12, 2018 (152)
69	ILLUMINA	ss3635337120	Oct 12, 2018 (152)
70	ILLUMINA	ss3636082884	Oct 12, 2018 (152)
71	ILLUMINA	ss3637087767	Oct 12, 2018 (152)
72	ILLUMINA	ss3640108429	Oct 12, 2018 (152)
73	URBANLAB	ss3649354399	Oct 12, 2018 (152)
74	EGCUT_WGS	ss3673820121	Jul 13, 2019 (153)
75	EVA_DECODE	ss3689779580	Jul 13, 2019 (153)
76	ACPOP	ss3737275870	Jul 13, 2019 (153)
77	ILLUMINA	ss3744701991	Jul 13, 2019 (153)
78	EVA	ss3748041570	Jul 13, 2019 (153)
79	ILLUMINA	ss3772202581	Jul 13, 2019 (153)
80	PACBIO	ss3786653888	Jul 13, 2019 (153)
81	PACBIO	ss3791836268	Jul 13, 2019 (153)
82	PACBIO	ss3796718335	Jul 13, 2019 (153)
83	KHV_HUMAN_GENOMES	ss3813413569	Jul 13, 2019 (153)
84	EVA	ss3832095438	Apr 26, 2020 (154)
85	EVA	ss3839582161	Apr 26, 2020 (154)
86	EVA	ss3845054060	Apr 26, 2020 (154)
87	SGDP_PRJ	ss3874064805	Apr 26, 2020 (154)
88	KRGDB	ss3922130002	Apr 26, 2020 (154)
89	KOGIC	ss3967775958	Apr 26, 2020 (154)
90	EVA	ss4017482938	Apr 26, 2021 (155)
91	TOPMED	ss4850625414	Apr 26, 2021 (155)
92	TOMMO_GENOMICS	ss5197378647	Apr 26, 2021 (155)
93	1000G_HIGH_COVERAGE	ss5283838568	Oct 16, 2022 (156)
94	EVA	ss5315469275	Oct 16, 2022 (156)
95	EVA	ss5393113901	Oct 16, 2022 (156)
96	HUGCELL_USP	ss5479474748	Oct 16, 2022 (156)
97	EVA	ss5509994269	Oct 16, 2022 (156)
98	1000G_HIGH_COVERAGE	ss5577671959	Oct 16, 2022 (156)
99	SANFORD_IMAGENETICS	ss5649172361	Oct 16, 2022 (156)
100	TOMMO_GENOMICS	ss5743126588	Oct 16, 2022 (156)
101	EVA	ss5799810910	Oct 16, 2022 (156)
102	YY_MCH	ss5811476663	Oct 16, 2022 (156)
103	EVA	ss5824320957	Oct 16, 2022 (156)
104	EVA	ss5849543222	Oct 16, 2022 (156)
105	EVA	ss5878709445	Oct 16, 2022 (156)
106	EVA	ss5940452014	Oct 16, 2022 (156)
107	1000Genomes	NC_000010.10 - 45126887	Oct 12, 2018 (152)
108	1000Genomes_30x	NC_000010.11 - 44631439	Oct 16, 2022 (156)
109	The Avon Longitudinal Study of Parents and Children	NC_000010.10 - 45126887	Oct 12, 2018 (152)
110	Chileans	NC_000010.10 - 45126887	Apr 26, 2020 (154)
111	Genetic variation in the Estonian population	NC_000010.10 - 45126887	Oct 12, 2018 (152)
112	The Danish reference pan genome	NC_000010.10 - 45126887	Apr 26, 2020 (154)
113	gnomAD - Genomes	NC_000010.11 - 44631439	Apr 26, 2021 (155)
114	Genome of the Netherlands Release 5	NC_000010.10 - 45126887	Apr 26, 2020 (154)
115	HapMap	NC_000010.11 - 44631439	Apr 26, 2020 (154)
116	KOREAN population from KRGDB	NC_000010.10 - 45126887	Apr 26, 2020 (154)
117	Korean Genome Project	NC_000010.11 - 44631439	Apr 26, 2020 (154)
118	Northern Sweden	NC_000010.10 - 45126887	Jul 13, 2019 (153)
119	Qatari	NC_000010.10 - 45126887	Apr 26, 2020 (154)
120	SGDP_PRJ	NC_000010.10 - 45126887	Apr 26, 2020 (154)
121	Siberian	NC_000010.10 - 45126887	Apr 26, 2020 (154)
122	8.3KJPN	NC_000010.10 - 45126887	Apr 26, 2021 (155)
123	14KJPN	NC_000010.11 - 44631439	Oct 16, 2022 (156)
124	TopMed	NC_000010.11 - 44631439	Apr 26, 2021 (155)
125	UK 10K study - Twins	NC_000010.10 - 45126887	Oct 12, 2018 (152)
126	A Vietnamese Genetic Variation Database	NC_000010.10 - 45126887	Jul 13, 2019 (153)
127	ALFA	NC_000010.11 - 44631439	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)
rs17409564	Oct 08, 2004 (123)
rs58379053	Feb 26, 2009 (130)
rs386508950	Aug 21, 2014 (142)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
6250964138	NC_000010.11:44631438:T:A	NC_000010.11:44631438:T:A	(self)
ss66217052, ss76363473, ss109397771, ss113180098, ss168268057, ss169789521, ss173387213, ss174514730, ss201451573, ss207170253, ss254269888, ss280594354, ss291027461, ss479160740, ss1597101342, ss1713175523	NC_000010.9:44446892:T:C	NC_000010.11:44631438:T:C	(self)
49615326, 27550280, 48952, 19558369, 2133715, 12282515, 29307396, 10560735, 12828590, 26081785, 6906865, 55347954, 27550280, 6114968, ss224695481, ss235153933, ss241864669, ss479162515, ss479479600, ss484381538, ss536566895, ss561922451, ss656644992, ss778344362, ss782637065, ss783606585, ss831887181, ss833799000, ss987436312, ss1076946670, ss1337235231, ss1426301916, ss1575079872, ss1624472601, ss1667466634, ss1751968998, ss1806364469, ss1930786660, ss1967114423, ss2026117586, ss2154390511, ss2627528145, ss2632705049, ss2698627035, ss2888168869, ss3006380255, ss3349092686, ss3626436363, ss3630731228, ss3632947493, ss3633644531, ss3634401087, ss3635337120, ss3636082884, ss3637087767, ss3640108429, ss3673820121, ss3737275870, ss3744701991, ss3748041570, ss3772202581, ss3786653888, ss3791836268, ss3796718335, ss3832095438, ss3839582161, ss3874064805, ss3922130002, ss4017482938, ss5197378647, ss5315469275, ss5393113901, ss5509994269, ss5649172361, ss5799810910, ss5824320957, ss5940452014	NC_000010.10:45126886:T:C	NC_000010.11:44631438:T:C	(self)
65197894, 350630307, 390110, 24153959, 76963692, 66171069, 6250964138, ss2174409265, ss3026847723, ss3649354399, ss3689779580, ss3813413569, ss3845054060, ss3967775958, ss4850625414, ss5283838568, ss5479474748, ss5577671959, ss5743126588, ss5811476663, ss5849543222, ss5878709445	NC_000010.11:44631438:T:C	NC_000010.11:44631438:T:C	(self)
ss19171098	NT_033985.6:2530199:T:C	NC_000010.11:44631438:T:C	(self)
ss1463401, ss6149136, ss24550372, ss38603237, ss65714023, ss68365900, ss81449941, ss97644066, ss138678463, ss154947975, ss159853255	NT_033985.7:2771951:T:C	NC_000010.11:44631438: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 rs1002589

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

rs1002589