Name: rs9341659
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.

rs9341659

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:77311249 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.467619 (123774/264690, TOPMED)
T=0.482002 (67406/139846, GnomAD)
T=0.38159 (10783/28258, 14KJPN) (+ 17 more)
C=0.47041 (8886/18890, ALFA)
T=0.38496 (6452/16760, 8.3KJPN)
T=0.4433 (2839/6404, 1000G_30x)
T=0.4435 (2221/5008, 1000G)
C=0.4071 (1824/4480, Estonian)
C=0.4312 (1662/3854, ALSPAC)
C=0.4094 (1518/3708, TWINSUK)
T=0.3901 (1143/2930, KOREAN)
T=0.3810 (698/1832, Korea1K)
C=0.423 (422/998, GoNL)
C=0.423 (254/600, NorthernSweden)
C=0.315 (117/372, SGDP_PRJ)
T=0.407 (132/324, HapMap)
C=0.463 (100/216, Qatari)
T=0.420 (89/212, Vietnamese)
C=0.31 (13/42, Siberian)
C=0.47 (19/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC101928570 : Intron 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	18890	C=0.47041	T=0.52959
European	Sub	14286	C=0.41145	T=0.58855
African	Sub	2946	C=0.7373	T=0.2627
African Others	Sub	114	C=0.763	T=0.237
African American	Sub	2832	C=0.7362	T=0.2638
Asian	Sub	112	C=0.562	T=0.438
East Asian	Sub	86	C=0.56	T=0.44
Other Asian	Sub	26	C=0.58	T=0.42
Latin American 1	Sub	146	C=0.507	T=0.493
Latin American 2	Sub	610	C=0.505	T=0.495
South Asian	Sub	98	C=0.36	T=0.64
Other	Sub	692	C=0.514	T=0.486

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=0.532381	T=0.467619
gnomAD - Genomes	Global	Study-wide	139846	C=0.517998	T=0.482002
gnomAD - Genomes	European	Sub	75772	C=0.40832	T=0.59168
gnomAD - Genomes	African	Sub	41880	C=0.72732	T=0.27268
gnomAD - Genomes	American	Sub	13614	C=0.49890	T=0.50110
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	C=0.4380	T=0.5620
gnomAD - Genomes	East Asian	Sub	3118	C=0.5532	T=0.4468
gnomAD - Genomes	Other	Sub	2142	C=0.4995	T=0.5005
14KJPN	JAPANESE	Study-wide	28258	C=0.61841	T=0.38159
Allele Frequency Aggregator	Total	Global	18890	C=0.47041	T=0.52959
Allele Frequency Aggregator	European	Sub	14286	C=0.41145	T=0.58855
Allele Frequency Aggregator	African	Sub	2946	C=0.7373	T=0.2627
Allele Frequency Aggregator	Other	Sub	692	C=0.514	T=0.486
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.505	T=0.495
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.507	T=0.493
Allele Frequency Aggregator	Asian	Sub	112	C=0.562	T=0.438
Allele Frequency Aggregator	South Asian	Sub	98	C=0.36	T=0.64
8.3KJPN	JAPANESE	Study-wide	16760	C=0.61504	T=0.38496
1000Genomes_30x	Global	Study-wide	6404	C=0.5567	T=0.4433
1000Genomes_30x	African	Sub	1786	C=0.7699	T=0.2301
1000Genomes_30x	Europe	Sub	1266	C=0.3878	T=0.6122
1000Genomes_30x	South Asian	Sub	1202	C=0.4393	T=0.5607
1000Genomes_30x	East Asian	Sub	1170	C=0.5581	T=0.4419
1000Genomes_30x	American	Sub	980	C=0.529	T=0.471
1000Genomes	Global	Study-wide	5008	C=0.5565	T=0.4435
1000Genomes	African	Sub	1322	C=0.7693	T=0.2307
1000Genomes	East Asian	Sub	1008	C=0.5734	T=0.4266
1000Genomes	Europe	Sub	1006	C=0.3877	T=0.6123
1000Genomes	South Asian	Sub	978	C=0.445	T=0.555
1000Genomes	American	Sub	694	C=0.529	T=0.471
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.4071	T=0.5929
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.4312	T=0.5688
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.4094	T=0.5906
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.6099	T=0.3901
Korean Genome Project	KOREAN	Study-wide	1832	C=0.6190	T=0.3810
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.423	T=0.577
Northern Sweden	ACPOP	Study-wide	600	C=0.423	T=0.577
SGDP_PRJ	Global	Study-wide	372	C=0.315	T=0.685
HapMap	Global	Study-wide	324	C=0.593	T=0.407
HapMap	American	Sub	120	C=0.383	T=0.617
HapMap	African	Sub	114	C=0.754	T=0.246
HapMap	Asian	Sub	90	C=0.67	T=0.33
Qatari	Global	Study-wide	216	C=0.463	T=0.537
A Vietnamese Genetic Variation Database	Global	Study-wide	212	C=0.580	T=0.420
Siberian	Global	Study-wide	42	C=0.31	T=0.69
The Danish reference pan genome	Danish	Study-wide	40	C=0.47	T=0.53

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 6	NC_000006.12:g.77311249C>T
GRCh37.p13 chr 6	NC_000006.11:g.78020966C>T

Gene: LOC101928570, uncharacterized LOC101928570 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC101928570 transcript variant X1	XR_001744205.2:n.	N/A	Intron Variant
LOC101928570 transcript variant X3	XR_001744206.2:n.	N/A	Intron Variant
LOC101928570 transcript variant X5	XR_001744207.2:n.	N/A	Intron Variant
LOC101928570 transcript variant X2	XR_007059650.1:n.	N/A	Intron Variant
LOC101928570 transcript variant X4	XR_241864.5:n.	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	C=	T
GRCh38.p14 chr 6	NC_000006.12:g.77311249=	NC_000006.12:g.77311249C>T
GRCh37.p13 chr 6	NC_000006.11:g.78020966=	NC_000006.11:g.78020966C>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#.

70 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss12779730	Dec 05, 2003 (119)
2	CSHL-HAPMAP	ss17134683	Feb 27, 2004 (120)
3	ABI	ss44689911	Mar 14, 2006 (126)
4	HGSV	ss77190565	Dec 07, 2007 (129)
5	BCMHGSC_JDW	ss93497550	Mar 24, 2008 (129)
6	BGI	ss104328936	Dec 01, 2009 (131)
7	1000GENOMES	ss110386857	Jan 24, 2009 (130)
8	1000GENOMES	ss114606112	Jan 25, 2009 (130)
9	ILLUMINA-UK	ss116558187	Feb 14, 2009 (130)
10	ENSEMBL	ss144074788	Dec 01, 2009 (131)
11	GMI	ss157178168	Dec 01, 2009 (131)
12	COMPLETE_GENOMICS	ss163779994	Jul 04, 2010 (132)
13	COMPLETE_GENOMICS	ss166909622	Jul 04, 2010 (132)
14	BCM-HGSC-SUB	ss207491966	Jul 04, 2010 (132)
15	1000GENOMES	ss222484976	Jul 14, 2010 (132)
16	1000GENOMES	ss233545223	Jul 15, 2010 (132)
17	1000GENOMES	ss240587421	Jul 15, 2010 (132)
18	BL	ss254477897	May 09, 2011 (134)
19	GMI	ss278879127	May 04, 2012 (137)
20	GMI	ss285444665	Apr 25, 2013 (138)
21	PJP	ss293641719	May 09, 2011 (134)
22	TISHKOFF	ss559308730	Apr 25, 2013 (138)
23	SSMP	ss653270622	Apr 25, 2013 (138)
24	EVA-GONL	ss983122814	Aug 21, 2014 (142)
25	JMKIDD_LAB	ss1073753314	Aug 21, 2014 (142)
26	1000GENOMES	ss1320847300	Aug 21, 2014 (142)
27	DDI	ss1430789145	Apr 01, 2015 (144)
28	EVA_GENOME_DK	ss1581749723	Apr 01, 2015 (144)
29	EVA_DECODE	ss1592667396	Apr 01, 2015 (144)
30	EVA_UK10K_ALSPAC	ss1615938892	Apr 01, 2015 (144)
31	EVA_UK10K_TWINSUK	ss1658932925	Apr 01, 2015 (144)
32	HAMMER_LAB	ss1804516139	Sep 08, 2015 (146)
33	WEILL_CORNELL_DGM	ss1926379592	Feb 12, 2016 (147)
34	GENOMED	ss1970441539	Jul 19, 2016 (147)
35	JJLAB	ss2023833071	Sep 14, 2016 (149)
36	USC_VALOUEV	ss2152025194	Dec 20, 2016 (150)
37	HUMAN_LONGEVITY	ss2285358279	Dec 20, 2016 (150)
38	SYSTEMSBIOZJU	ss2626411140	Nov 08, 2017 (151)
39	GRF	ss2707637735	Nov 08, 2017 (151)
40	GNOMAD	ss2841006294	Nov 08, 2017 (151)
41	SWEGEN	ss2999375029	Nov 08, 2017 (151)
42	BIOINF_KMB_FNS_UNIBA	ss3025709550	Nov 08, 2017 (151)
43	CSHL	ss3347062665	Nov 08, 2017 (151)
44	EGCUT_WGS	ss3667246608	Jul 13, 2019 (153)
45	EVA_DECODE	ss3717569711	Jul 13, 2019 (153)
46	ACPOP	ss3733668372	Jul 13, 2019 (153)
47	EVA	ss3765235126	Jul 13, 2019 (153)
48	PACBIO	ss3785525080	Jul 13, 2019 (153)
49	PACBIO	ss3790868334	Jul 13, 2019 (153)
50	PACBIO	ss3795747414	Jul 13, 2019 (153)
51	KHV_HUMAN_GENOMES	ss3808385128	Jul 13, 2019 (153)
52	EVA	ss3830017573	Apr 26, 2020 (154)
53	EVA	ss3838489867	Apr 26, 2020 (154)
54	EVA	ss3843937198	Apr 26, 2020 (154)
55	SGDP_PRJ	ss3864958610	Apr 26, 2020 (154)
56	KRGDB	ss3911835543	Apr 26, 2020 (154)
57	KOGIC	ss3959393485	Apr 26, 2020 (154)
58	TOPMED	ss4709230708	Apr 26, 2021 (155)
59	TOMMO_GENOMICS	ss5178313831	Apr 26, 2021 (155)
60	1000G_HIGH_COVERAGE	ss5269088304	Oct 13, 2022 (156)
61	HUGCELL_USP	ss5466663133	Oct 13, 2022 (156)
62	EVA	ss5508570112	Oct 13, 2022 (156)
63	1000G_HIGH_COVERAGE	ss5555351857	Oct 13, 2022 (156)
64	SANFORD_IMAGENETICS	ss5640768479	Oct 13, 2022 (156)
65	TOMMO_GENOMICS	ss5716732076	Oct 13, 2022 (156)
66	YY_MCH	ss5807641596	Oct 13, 2022 (156)
67	EVA	ss5842502171	Oct 13, 2022 (156)
68	EVA	ss5855430410	Oct 13, 2022 (156)
69	EVA	ss5884519342	Oct 13, 2022 (156)
70	EVA	ss5969265923	Oct 13, 2022 (156)
71	1000Genomes	NC_000006.11 - 78020966	Oct 12, 2018 (152)
72	1000Genomes_30x	NC_000006.12 - 77311249	Oct 13, 2022 (156)
73	The Avon Longitudinal Study of Parents and Children	NC_000006.11 - 78020966	Oct 12, 2018 (152)
74	Genetic variation in the Estonian population	NC_000006.11 - 78020966	Oct 12, 2018 (152)
75	The Danish reference pan genome	NC_000006.11 - 78020966	Apr 26, 2020 (154)
76	gnomAD - Genomes	NC_000006.12 - 77311249	Apr 26, 2021 (155)
77	Genome of the Netherlands Release 5	NC_000006.11 - 78020966	Apr 26, 2020 (154)
78	HapMap	NC_000006.12 - 77311249	Apr 26, 2020 (154)
79	KOREAN population from KRGDB	NC_000006.11 - 78020966	Apr 26, 2020 (154)
80	Korean Genome Project	NC_000006.12 - 77311249	Apr 26, 2020 (154)
81	Northern Sweden	NC_000006.11 - 78020966	Jul 13, 2019 (153)
82	Qatari	NC_000006.11 - 78020966	Apr 26, 2020 (154)
83	SGDP_PRJ	NC_000006.11 - 78020966	Apr 26, 2020 (154)
84	Siberian	NC_000006.11 - 78020966	Apr 26, 2020 (154)
85	8.3KJPN	NC_000006.11 - 78020966	Apr 26, 2021 (155)
86	14KJPN	NC_000006.12 - 77311249	Oct 13, 2022 (156)
87	TopMed	NC_000006.12 - 77311249	Apr 26, 2021 (155)
88	UK 10K study - Twins	NC_000006.11 - 78020966	Oct 12, 2018 (152)
89	A Vietnamese Genetic Variation Database	NC_000006.11 - 78020966	Jul 13, 2019 (153)
90	ALFA	NC_000006.12 - 77311249	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
ss77190565	NC_000006.9:78077684:C:T	NC_000006.12:77311248:C:T	(self)
ss93497550, ss110386857, ss114606112, ss116558187, ss163779994, ss166909622, ss207491966, ss254477897, ss278879127, ss285444665, ss293641719, ss1592667396	NC_000006.10:78077684:C:T	NC_000006.12:77311248:C:T	(self)
32661737, 18194837, 12984856, 7914662, 8106774, 19012937, 6953237, 8421522, 16975590, 4541548, 36283138, 18194837, 4043914, ss222484976, ss233545223, ss240587421, ss559308730, ss653270622, ss983122814, ss1073753314, ss1320847300, ss1430789145, ss1581749723, ss1615938892, ss1658932925, ss1804516139, ss1926379592, ss1970441539, ss2023833071, ss2152025194, ss2626411140, ss2707637735, ss2841006294, ss2999375029, ss3347062665, ss3667246608, ss3733668372, ss3765235126, ss3785525080, ss3790868334, ss3795747414, ss3830017573, ss3838489867, ss3864958610, ss3911835543, ss5178313831, ss5508570112, ss5640768479, ss5842502171, ss5969265923	NC_000006.11:78020965:C:T	NC_000006.12:77311248:C:T	(self)
42877792, 230506965, 3169835, 15771486, 50569180, 546608266, 10159190276, ss2285358279, ss3025709550, ss3717569711, ss3808385128, ss3843937198, ss3959393485, ss4709230708, ss5269088304, ss5466663133, ss5555351857, ss5716732076, ss5807641596, ss5855430410, ss5884519342	NC_000006.12:77311248:C:T	NC_000006.12:77311248:C:T	(self)
ss12779730, ss17134683	NT_007299.12:15841136:C:T	NC_000006.12:77311248:C:T	(self)
ss44689911, ss104328936, ss144074788, ss157178168	NT_007299.13:16140799:C:T	NC_000006.12:77311248: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 rs9341659

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

rs9341659