Name: rs9290069
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.

rs9290069

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr3:161173158 (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>G / A>T
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.414628 (109748/264690, TOPMED)
A=0.434876 (60894/140026, GnomAD)
A=0.18947 (5354/28258, 14KJPN) (+ 18 more)
A=0.18658 (3127/16760, 8.3KJPN)
G=0.3603 (3444/9560, ALFA)
A=0.3431 (2197/6404, 1000G_30x)
A=0.3403 (1704/5008, 1000G)
G=0.4877 (2185/4480, Estonian)
G=0.4751 (1831/3854, ALSPAC)
G=0.4827 (1790/3708, TWINSUK)
A=0.1543 (452/2930, KOREAN)
A=0.1578 (289/1832, Korea1K)
G=0.457 (456/998, GoNL)
A=0.472 (283/600, NorthernSweden)
A=0.217 (107/492, SGDP_PRJ)
A=0.481 (104/216, Qatari)
A=0.173 (37/214, Vietnamese)
A=0.324 (61/188, HapMap)
A=0.20 (10/50, Siberian)
A=0.50 (20/40, GENOME_DK)
G=0.50 (20/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC124906300 : Intron Variant
LOC105374186 : 500B Downstream Variant
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	9560	A=0.6397	G=0.3603, T=0.0000
European	Sub	8688	A=0.6276	G=0.3724, T=0.0000
African	Sub	440	A=0.811	G=0.189, T=0.000
African Others	Sub	30	A=0.90	G=0.10, T=0.00
African American	Sub	410	A=0.805	G=0.195, T=0.000
Asian	Sub	8	A=0.8	G=0.2, T=0.0
East Asian	Sub	4	A=0.5	G=0.5, T=0.0
Other Asian	Sub	4	A=1.0	G=0.0, T=0.0
Latin American 1	Sub	34	A=1.00	G=0.00, T=0.00
Latin American 2	Sub	66	A=1.00	G=0.00, T=0.00
South Asian	Sub	12	A=0.75	G=0.25, T=0.00
Other	Sub	312	A=0.612	G=0.388, 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=0.414628	G=0.585372
gnomAD - Genomes	Global	Study-wide	140026	A=0.434876	G=0.565124
gnomAD - Genomes	European	Sub	75836	A=0.51814	G=0.48186
gnomAD - Genomes	African	Sub	41938	A=0.31911	G=0.68089
gnomAD - Genomes	American	Sub	13648	A=0.38753	G=0.61247
gnomAD - Genomes	Ashkenazi Jewish	Sub	3316	A=0.4475	G=0.5525
gnomAD - Genomes	East Asian	Sub	3134	A=0.1615	G=0.8385
gnomAD - Genomes	Other	Sub	2154	A=0.4355	G=0.5645
14KJPN	JAPANESE	Study-wide	28258	A=0.18947	G=0.81053
8.3KJPN	JAPANESE	Study-wide	16760	A=0.18658	G=0.81342
Allele Frequency Aggregator	Total	Global	9560	A=0.6397	G=0.3603, T=0.0000
Allele Frequency Aggregator	European	Sub	8688	A=0.6276	G=0.3724, T=0.0000
Allele Frequency Aggregator	African	Sub	440	A=0.811	G=0.189, T=0.000
Allele Frequency Aggregator	Other	Sub	312	A=0.612	G=0.388, T=0.000
Allele Frequency Aggregator	Latin American 2	Sub	66	A=1.00	G=0.00, T=0.00
Allele Frequency Aggregator	Latin American 1	Sub	34	A=1.00	G=0.00, T=0.00
Allele Frequency Aggregator	South Asian	Sub	12	A=0.75	G=0.25, T=0.00
Allele Frequency Aggregator	Asian	Sub	8	A=0.8	G=0.2, T=0.0
1000Genomes_30x	Global	Study-wide	6404	A=0.3431	G=0.6569
1000Genomes_30x	African	Sub	1786	A=0.3046	G=0.6954
1000Genomes_30x	Europe	Sub	1266	A=0.5166	G=0.4834
1000Genomes_30x	South Asian	Sub	1202	A=0.3877	G=0.6123
1000Genomes_30x	East Asian	Sub	1170	A=0.1701	G=0.8299
1000Genomes_30x	American	Sub	980	A=0.341	G=0.659
1000Genomes	Global	Study-wide	5008	A=0.3403	G=0.6597
1000Genomes	African	Sub	1322	A=0.3101	G=0.6899
1000Genomes	East Asian	Sub	1008	A=0.1657	G=0.8343
1000Genomes	Europe	Sub	1006	A=0.5179	G=0.4821
1000Genomes	South Asian	Sub	978	A=0.380	G=0.620
1000Genomes	American	Sub	694	A=0.337	G=0.663
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.5123	G=0.4877
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.5249	G=0.4751
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.5173	G=0.4827
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.1543	G=0.8457
Korean Genome Project	KOREAN	Study-wide	1832	A=0.1578	G=0.8422
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.543	G=0.457
Northern Sweden	ACPOP	Study-wide	600	A=0.472	G=0.528
SGDP_PRJ	Global	Study-wide	492	A=0.217	G=0.783
Qatari	Global	Study-wide	216	A=0.481	G=0.519
A Vietnamese Genetic Variation Database	Global	Study-wide	214	A=0.173	G=0.827
HapMap	Global	Study-wide	188	A=0.324	G=0.676
HapMap	African	Sub	112	A=0.384	G=0.616
HapMap	Asian	Sub	76	A=0.24	G=0.76
Siberian	Global	Study-wide	50	A=0.20	G=0.80
The Danish reference pan genome	Danish	Study-wide	40	A=0.50	G=0.50

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.161173158A>G
GRCh38.p14 chr 3	NC_000003.12:g.161173158A>T
GRCh37.p13 chr 3	NC_000003.11:g.160890946A>G
GRCh37.p13 chr 3	NC_000003.11:g.160890946A>T

Gene: LOC124906300, uncharacterized LOC124906300 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC124906300 transcript variant X1	XR_007096148.1:n.	N/A	Intron Variant

Gene: LOC105374186, uncharacterized LOC105374186 (minus strand) : 500B Downstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105374186 transcript	XR_007096149.1:n.	N/A	Downstream Transcript 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=	G	T
GRCh38.p14 chr 3	NC_000003.12:g.161173158=	NC_000003.12:g.161173158A>G	NC_000003.12:g.161173158A>T
GRCh37.p13 chr 3	NC_000003.11:g.160890946=	NC_000003.11:g.160890946A>G	NC_000003.11:g.160890946A>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#.

71 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCM_SSAHASNP	ss13696246	Dec 05, 2003 (119)
2	WUGSC_SSAHASNP	ss13828731	Dec 05, 2003 (119)
3	CSHL-HAPMAP	ss20174462	Feb 27, 2004 (120)
4	SSAHASNP	ss21934599	Apr 05, 2004 (121)
5	ABI	ss42021560	Mar 14, 2006 (126)
6	BCMHGSC_JDW	ss92348392	Mar 24, 2008 (129)
7	HUMANGENOME_JCVI	ss96068811	Feb 06, 2009 (130)
8	BGI	ss104003511	Dec 01, 2009 (131)
9	1000GENOMES	ss111234298	Jan 25, 2009 (130)
10	1000GENOMES	ss112630757	Jan 25, 2009 (130)
11	ENSEMBL	ss135449742	Dec 01, 2009 (131)
12	GMI	ss156422801	Dec 01, 2009 (131)
13	COMPLETE_GENOMICS	ss164782366	Jul 04, 2010 (132)
14	BUSHMAN	ss203438815	Jul 04, 2010 (132)
15	BCM-HGSC-SUB	ss206083620	Jul 04, 2010 (132)
16	1000GENOMES	ss220538260	Jul 14, 2010 (132)
17	1000GENOMES	ss232112407	Jul 14, 2010 (132)
18	1000GENOMES	ss239466740	Jul 15, 2010 (132)
19	GMI	ss277427388	May 04, 2012 (137)
20	GMI	ss284784088	Apr 25, 2013 (138)
21	PJP	ss292959898	May 09, 2011 (134)
22	TISHKOFF	ss557072279	Apr 25, 2013 (138)
23	SSMP	ss650809811	Apr 25, 2013 (138)
24	EVA-GONL	ss979376241	Aug 21, 2014 (142)
25	JMKIDD_LAB	ss1070994394	Aug 21, 2014 (142)
26	1000GENOMES	ss1306982278	Aug 21, 2014 (142)
27	DDI	ss1429648571	Apr 01, 2015 (144)
28	EVA_GENOME_DK	ss1580265011	Apr 01, 2015 (144)
29	EVA_UK10K_ALSPAC	ss1608651919	Apr 01, 2015 (144)
30	EVA_UK10K_TWINSUK	ss1651645952	Apr 01, 2015 (144)
31	HAMMER_LAB	ss1800327935	Sep 08, 2015 (146)
32	WEILL_CORNELL_DGM	ss1922599652	Feb 12, 2016 (147)
33	GENOMED	ss1969570704	Jul 19, 2016 (147)
34	JJLAB	ss2021872530	Sep 14, 2016 (149)
35	USC_VALOUEV	ss2149968269	Dec 20, 2016 (150)
36	HUMAN_LONGEVITY	ss2257547690	Dec 20, 2016 (150)
37	SYSTEMSBIOZJU	ss2625437318	Nov 08, 2017 (151)
38	GRF	ss2705386976	Nov 08, 2017 (151)
39	GNOMAD	ss2801494009	Nov 08, 2017 (151)
40	SWEGEN	ss2993525199	Nov 08, 2017 (151)
41	BIOINF_KMB_FNS_UNIBA	ss3024703376	Nov 08, 2017 (151)
42	CSHL	ss3345360236	Nov 08, 2017 (151)
43	URBANLAB	ss3647569664	Oct 12, 2018 (152)
44	EGCUT_WGS	ss3661466224	Jul 13, 2019 (153)
45	EVA_DECODE	ss3710685022	Jul 13, 2019 (153)
46	ACPOP	ss3730528496	Jul 13, 2019 (153)
47	EVA	ss3760945339	Jul 13, 2019 (153)
48	PACBIO	ss3784518518	Jul 13, 2019 (153)
49	PACBIO	ss3790003282	Jul 13, 2019 (153)
50	PACBIO	ss3794877920	Jul 13, 2019 (153)
51	KHV_HUMAN_GENOMES	ss3804079677	Jul 13, 2019 (153)
52	EVA	ss3828177482	Apr 25, 2020 (154)
53	EVA	ss3837521881	Apr 25, 2020 (154)
54	EVA	ss3842953581	Apr 25, 2020 (154)
55	SGDP_PRJ	ss3857403437	Apr 25, 2020 (154)
56	KRGDB	ss3903460000	Apr 25, 2020 (154)
57	KOGIC	ss3952806953	Apr 25, 2020 (154)
58	TOPMED	ss4590839469	Apr 26, 2021 (155)
59	TOMMO_GENOMICS	ss5162512313	Apr 26, 2021 (155)
60	1000G_HIGH_COVERAGE	ss5256745987	Oct 12, 2022 (156)
61	EVA	ss5344585448	Oct 12, 2022 (156)
62	HUGCELL_USP	ss5455812766	Oct 12, 2022 (156)
63	EVA	ss5507278818	Oct 12, 2022 (156)
64	1000G_HIGH_COVERAGE	ss5536559278	Oct 12, 2022 (156)
65	SANFORD_IMAGENETICS	ss5633599124	Oct 12, 2022 (156)
66	TOMMO_GENOMICS	ss5695658089	Oct 12, 2022 (156)
67	YY_MCH	ss5804425195	Oct 12, 2022 (156)
68	EVA	ss5826756697	Oct 12, 2022 (156)
69	EVA	ss5853925163	Oct 12, 2022 (156)
70	EVA	ss5871830350	Oct 12, 2022 (156)
71	EVA	ss5961968948	Oct 12, 2022 (156)
72	1000Genomes	NC_000003.11 - 160890946	Oct 12, 2018 (152)
73	1000Genomes_30x	NC_000003.12 - 161173158	Oct 12, 2022 (156)
74	The Avon Longitudinal Study of Parents and Children	NC_000003.11 - 160890946	Oct 12, 2018 (152)
75	Genetic variation in the Estonian population	NC_000003.11 - 160890946	Oct 12, 2018 (152)
76	The Danish reference pan genome	NC_000003.11 - 160890946	Apr 25, 2020 (154)
77	gnomAD - Genomes	NC_000003.12 - 161173158	Apr 26, 2021 (155)
78	Genome of the Netherlands Release 5	NC_000003.11 - 160890946	Apr 25, 2020 (154)
79	HapMap	NC_000003.12 - 161173158	Apr 25, 2020 (154)
80	KOREAN population from KRGDB	NC_000003.11 - 160890946	Apr 25, 2020 (154)
81	Korean Genome Project	NC_000003.12 - 161173158	Apr 25, 2020 (154)
82	Northern Sweden	NC_000003.11 - 160890946	Jul 13, 2019 (153)
83	Qatari	NC_000003.11 - 160890946	Apr 25, 2020 (154)
84	SGDP_PRJ	NC_000003.11 - 160890946	Apr 25, 2020 (154)
85	Siberian	NC_000003.11 - 160890946	Apr 25, 2020 (154)
86	8.3KJPN	NC_000003.11 - 160890946	Apr 26, 2021 (155)
87	14KJPN	NC_000003.12 - 161173158	Oct 12, 2022 (156)
88	TopMed	NC_000003.12 - 161173158	Apr 26, 2021 (155)
89	UK 10K study - Twins	NC_000003.11 - 160890946	Oct 12, 2018 (152)
90	A Vietnamese Genetic Variation Database	NC_000003.11 - 160890946	Jul 13, 2019 (153)
91	ALFA	NC_000003.12 - 161173158	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss92348392, ss111234298, ss112630757, ss164782366, ss203438815, ss206083620, ss277427388, ss284784088, ss292959898	NC_000003.10:162373639:A:G	NC_000003.12:161173157:A:G	(self)
18276508, 10183586, 7204472, 6429950, 4472762, 10637394, 3813361, 4641582, 9420417, 2484623, 20481620, 10183586, 2222747, ss220538260, ss232112407, ss239466740, ss557072279, ss650809811, ss979376241, ss1070994394, ss1306982278, ss1429648571, ss1580265011, ss1608651919, ss1651645952, ss1800327935, ss1922599652, ss1969570704, ss2021872530, ss2149968269, ss2625437318, ss2705386976, ss2801494009, ss2993525199, ss3345360236, ss3661466224, ss3730528496, ss3760945339, ss3784518518, ss3790003282, ss3794877920, ss3828177482, ss3837521881, ss3857403437, ss3903460000, ss5162512313, ss5344585448, ss5507278818, ss5633599124, ss5826756697, ss5961968948	NC_000003.11:160890945:A:G	NC_000003.12:161173157:A:G	(self)
24085213, 129827763, 2496086, 9184954, 29495193, 428217024, 8111166420, ss2257547690, ss3024703376, ss3647569664, ss3710685022, ss3804079677, ss3842953581, ss3952806953, ss4590839469, ss5256745987, ss5455812766, ss5536559278, ss5695658089, ss5804425195, ss5853925163, ss5871830350	NC_000003.12:161173157:A:G	NC_000003.12:161173157:A:G	(self)
ss13696246, ss13828731, ss20174462, ss21934599	NT_005612.14:67386103:A:G	NC_000003.12:161173157:A:G	(self)
ss42021560, ss96068811, ss104003511, ss135449742, ss156422801	NT_005612.16:67386091:A:G	NC_000003.12:161173157:A:G	(self)
8111166420	NC_000003.12:161173157:A:T	NC_000003.12:161173157:A: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 rs9290069

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

rs9290069