Name: rs9442679
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.

rs9442679

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:71559539 (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=0.487873 (129135/264690, TOPMED)
C=0.495327 (69316/139940, GnomAD)
C=0.43054 (30454/70734, ALFA) (+ 18 more)
T=0.35144 (9931/28258, 14KJPN)
T=0.34911 (5851/16760, 8.3KJPN)
T=0.4185 (2680/6404, 1000G_30x)
T=0.4201 (2104/5008, 1000G)
C=0.3719 (1666/4480, Estonian)
C=0.3679 (1418/3854, ALSPAC)
C=0.3900 (1446/3708, TWINSUK)
T=0.3379 (990/2930, KOREAN)
T=0.4501 (938/2084, HGDP_Stanford)
T=0.3851 (724/1880, HapMap)
C=0.386 (385/998, GoNL)
C=0.373 (224/600, NorthernSweden)
C=0.362 (128/354, SGDP_PRJ)
T=0.486 (105/216, Qatari)
T=0.301 (65/216, Vietnamese)
C=0.28 (15/54, Siberian)
C=0.47 (19/40, GENOME_DK)
C=0.3 (2/6, Ancient Sardinia)

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	70734	C=0.43054	T=0.56946
European	Sub	59396	C=0.39910	T=0.60090
African	Sub	3280	C=0.8274	T=0.1726
African Others	Sub	136	C=0.853	T=0.147
African American	Sub	3144	C=0.8263	T=0.1737
Asian	Sub	132	C=0.818	T=0.182
East Asian	Sub	108	C=0.815	T=0.185
Other Asian	Sub	24	C=0.83	T=0.17
Latin American 1	Sub	154	C=0.578	T=0.422
Latin American 2	Sub	872	C=0.560	T=0.440
South Asian	Sub	4894	C=0.4902	T=0.5098
Other	Sub	2006	C=0.4741	T=0.5259

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=0.512127	T=0.487873
gnomAD - Genomes	Global	Study-wide	139940	C=0.495327	T=0.504673
gnomAD - Genomes	European	Sub	75790	C=0.38290	T=0.61710
gnomAD - Genomes	African	Sub	41914	C=0.70222	T=0.29778
gnomAD - Genomes	American	Sub	13640	C=0.46965	T=0.53035
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.3878	T=0.6122
gnomAD - Genomes	East Asian	Sub	3122	C=0.6694	T=0.3306
gnomAD - Genomes	Other	Sub	2150	C=0.5014	T=0.4986
Allele Frequency Aggregator	Total	Global	70734	C=0.43054	T=0.56946
Allele Frequency Aggregator	European	Sub	59396	C=0.39910	T=0.60090
Allele Frequency Aggregator	South Asian	Sub	4894	C=0.4902	T=0.5098
Allele Frequency Aggregator	African	Sub	3280	C=0.8274	T=0.1726
Allele Frequency Aggregator	Other	Sub	2006	C=0.4741	T=0.5259
Allele Frequency Aggregator	Latin American 2	Sub	872	C=0.560	T=0.440
Allele Frequency Aggregator	Latin American 1	Sub	154	C=0.578	T=0.422
Allele Frequency Aggregator	Asian	Sub	132	C=0.818	T=0.182
14KJPN	JAPANESE	Study-wide	28258	C=0.64856	T=0.35144
8.3KJPN	JAPANESE	Study-wide	16760	C=0.65089	T=0.34911
1000Genomes_30x	Global	Study-wide	6404	C=0.5815	T=0.4185
1000Genomes_30x	African	Sub	1786	C=0.7727	T=0.2273
1000Genomes_30x	Europe	Sub	1266	C=0.3697	T=0.6303
1000Genomes_30x	South Asian	Sub	1202	C=0.5591	T=0.4409
1000Genomes_30x	East Asian	Sub	1170	C=0.6393	T=0.3607
1000Genomes_30x	American	Sub	980	C=0.465	T=0.535
1000Genomes	Global	Study-wide	5008	C=0.5799	T=0.4201
1000Genomes	African	Sub	1322	C=0.7632	T=0.2368
1000Genomes	East Asian	Sub	1008	C=0.6429	T=0.3571
1000Genomes	Europe	Sub	1006	C=0.3618	T=0.6382
1000Genomes	South Asian	Sub	978	C=0.567	T=0.433
1000Genomes	American	Sub	694	C=0.473	T=0.527
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.3719	T=0.6281
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.3679	T=0.6321
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.3900	T=0.6100
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.6621	T=0.3379
HGDP-CEPH-db Supplement 1	Global	Study-wide	2084	C=0.5499	T=0.4501
HGDP-CEPH-db Supplement 1	Est_Asia	Sub	470	C=0.617	T=0.383
HGDP-CEPH-db Supplement 1	Central_South_Asia	Sub	414	C=0.454	T=0.546
HGDP-CEPH-db Supplement 1	Middle_Est	Sub	350	C=0.434	T=0.566
HGDP-CEPH-db Supplement 1	Europe	Sub	320	C=0.384	T=0.616
HGDP-CEPH-db Supplement 1	Africa	Sub	242	C=0.736	T=0.264
HGDP-CEPH-db Supplement 1	America	Sub	216	C=0.718	T=0.282
HGDP-CEPH-db Supplement 1	Oceania	Sub	72	C=0.83	T=0.17
HapMap	Global	Study-wide	1880	C=0.6149	T=0.3851
HapMap	American	Sub	766	C=0.533	T=0.467
HapMap	African	Sub	688	C=0.759	T=0.241
HapMap	Asian	Sub	250	C=0.636	T=0.364
HapMap	Europe	Sub	176	C=0.381	T=0.619
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.386	T=0.614
Northern Sweden	ACPOP	Study-wide	600	C=0.373	T=0.627
SGDP_PRJ	Global	Study-wide	354	C=0.362	T=0.638
Qatari	Global	Study-wide	216	C=0.514	T=0.486
A Vietnamese Genetic Variation Database	Global	Study-wide	216	C=0.699	T=0.301
Siberian	Global	Study-wide	54	C=0.28	T=0.72
The Danish reference pan genome	Danish	Study-wide	40	C=0.47	T=0.53
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	6	C=0.3	T=0.7

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.71559539C>T
GRCh37.p13 chr 6	NC_000006.11:g.72269242C>T

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.71559539=	NC_000006.12:g.71559539C>T
GRCh37.p13 chr 6	NC_000006.11:g.72269242=	NC_000006.11:g.72269242C>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#.

104 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss13053140	Dec 05, 2003 (119)
2	CSHL-HAPMAP	ss19673789	Feb 27, 2004 (120)
3	SSAHASNP	ss22370036	Apr 05, 2004 (121)
4	ILLUMINA	ss66630212	Nov 29, 2006 (127)
5	ILLUMINA	ss67918053	Nov 29, 2006 (127)
6	ILLUMINA	ss68042970	Nov 29, 2006 (127)
7	ILLUMINA	ss71607624	May 17, 2007 (127)
8	ILLUMINA	ss75457832	Dec 07, 2007 (129)
9	HGSV	ss77596396	Dec 07, 2007 (129)
10	ILLUMINA	ss79296591	Dec 15, 2007 (130)
11	KRIBB_YJKIM	ss84819428	Dec 15, 2007 (130)
12	BCMHGSC_JDW	ss93489554	Mar 24, 2008 (129)
13	ILLUMINA	ss98259562	May 25, 2008 (130)
14	HUMANGENOME_JCVI	ss98508493	Feb 05, 2009 (130)
15	1000GENOMES	ss110318821	Jan 24, 2009 (130)
16	1000GENOMES	ss114545961	Jan 25, 2009 (130)
17	ILLUMINA	ss122993136	Dec 01, 2009 (131)
18	ENSEMBL	ss144044472	Dec 01, 2009 (131)
19	ILLUMINA	ss154494086	Dec 01, 2009 (131)
20	ILLUMINA	ss159668098	Dec 01, 2009 (131)
21	COMPLETE_GENOMICS	ss163699056	Jul 04, 2010 (132)
22	COMPLETE_GENOMICS	ss166863346	Jul 04, 2010 (132)
23	ILLUMINA	ss172464922	Jul 04, 2010 (132)
24	ILLUMINA	ss174842680	Jul 04, 2010 (132)
25	BUSHMAN	ss202003811	Jul 04, 2010 (132)
26	BCM-HGSC-SUB	ss207631819	Jul 04, 2010 (132)
27	1000GENOMES	ss222464252	Jul 14, 2010 (132)
28	1000GENOMES	ss233529276	Jul 15, 2010 (132)
29	1000GENOMES	ss240573520	Jul 15, 2010 (132)
30	GMI	ss278861261	May 04, 2012 (137)
31	GMI	ss285436296	Apr 25, 2013 (138)
32	PJP	ss293633140	May 09, 2011 (134)
33	ILLUMINA	ss410867567	Sep 17, 2011 (135)
34	ILLUMINA	ss483542772	May 04, 2012 (137)
35	ILLUMINA	ss485279311	May 04, 2012 (137)
36	ILLUMINA	ss535749903	Sep 08, 2015 (146)
37	TISHKOFF	ss559284499	Apr 25, 2013 (138)
38	SSMP	ss653240925	Apr 25, 2013 (138)
39	ILLUMINA	ss780316908	Sep 08, 2015 (146)
40	ILLUMINA	ss782214924	Sep 08, 2015 (146)
41	ILLUMINA	ss825627109	Jul 19, 2016 (147)
42	ILLUMINA	ss833178843	Jul 13, 2019 (153)
43	ILLUMINA	ss835803977	Sep 08, 2015 (146)
44	EVA-GONL	ss983079227	Aug 21, 2014 (142)
45	JMKIDD_LAB	ss1073720859	Aug 21, 2014 (142)
46	1000GENOMES	ss1320681757	Aug 21, 2014 (142)
47	DDI	ss1430776318	Apr 01, 2015 (144)
48	EVA_GENOME_DK	ss1581732337	Apr 01, 2015 (144)
49	EVA_DECODE	ss1592621517	Apr 01, 2015 (144)
50	EVA_UK10K_ALSPAC	ss1615854222	Apr 01, 2015 (144)
51	EVA_UK10K_TWINSUK	ss1658848255	Apr 01, 2015 (144)
52	EVA_SVP	ss1712872059	Apr 01, 2015 (144)
53	HAMMER_LAB	ss1804497061	Sep 08, 2015 (146)
54	WEILL_CORNELL_DGM	ss1926335652	Feb 12, 2016 (147)
55	GENOMED	ss1970431307	Jul 19, 2016 (147)
56	JJLAB	ss2023809854	Sep 14, 2016 (149)
57	USC_VALOUEV	ss2152001646	Dec 20, 2016 (150)
58	HUMAN_LONGEVITY	ss2285023701	Dec 20, 2016 (150)
59	SYSTEMSBIOZJU	ss2626399403	Nov 08, 2017 (151)
60	ILLUMINA	ss2634466886	Nov 08, 2017 (151)
61	ILLUMINA	ss2635158490	Nov 08, 2017 (151)
62	GRF	ss2707610375	Nov 08, 2017 (151)
63	GNOMAD	ss2840535822	Nov 08, 2017 (151)
64	SWEGEN	ss2999305705	Nov 08, 2017 (151)
65	BIOINF_KMB_FNS_UNIBA	ss3025698149	Nov 08, 2017 (151)
66	CSHL	ss3347043075	Nov 08, 2017 (151)
67	ILLUMINA	ss3629574575	Oct 12, 2018 (152)
68	ILLUMINA	ss3632382437	Oct 12, 2018 (152)
69	ILLUMINA	ss3638637153	Oct 12, 2018 (152)
70	ILLUMINA	ss3639318997	Oct 12, 2018 (152)
71	ILLUMINA	ss3639685620	Oct 12, 2018 (152)
72	ILLUMINA	ss3642496659	Oct 12, 2018 (152)
73	ILLUMINA	ss3643577718	Oct 12, 2018 (152)
74	URBANLAB	ss3648383981	Oct 12, 2018 (152)
75	EGCUT_WGS	ss3667174860	Jul 13, 2019 (153)
76	EVA_DECODE	ss3717487742	Jul 13, 2019 (153)
77	ACPOP	ss3733630501	Jul 13, 2019 (153)
78	EVA	ss3765185405	Jul 13, 2019 (153)
79	PACBIO	ss3785513035	Jul 13, 2019 (153)
80	PACBIO	ss3790858172	Jul 13, 2019 (153)
81	PACBIO	ss3795737229	Jul 13, 2019 (153)
82	KHV_HUMAN_GENOMES	ss3808333973	Jul 13, 2019 (153)
83	EVA	ss3829996808	Apr 26, 2020 (154)
84	EVA	ss3838478254	Apr 26, 2020 (154)
85	EVA	ss3843925304	Apr 26, 2020 (154)
86	HGDP	ss3847838014	Apr 26, 2020 (154)
87	SGDP_PRJ	ss3864871231	Apr 26, 2020 (154)
88	KRGDB	ss3911737808	Apr 26, 2020 (154)
89	EVA	ss3985229846	Apr 26, 2021 (155)
90	EVA	ss4017281289	Apr 26, 2021 (155)
91	TOPMED	ss4707821520	Apr 26, 2021 (155)
92	TOMMO_GENOMICS	ss5178124791	Apr 26, 2021 (155)
93	1000G_HIGH_COVERAGE	ss5268943203	Oct 17, 2022 (156)
94	EVA	ss5315164532	Oct 17, 2022 (156)
95	HUGCELL_USP	ss5466538117	Oct 17, 2022 (156)
96	EVA	ss5508553129	Oct 17, 2022 (156)
97	1000G_HIGH_COVERAGE	ss5555129232	Oct 17, 2022 (156)
98	SANFORD_IMAGENETICS	ss5640684222	Oct 17, 2022 (156)
99	TOMMO_GENOMICS	ss5716490934	Oct 17, 2022 (156)
100	YY_MCH	ss5807602987	Oct 17, 2022 (156)
101	EVA	ss5842445558	Oct 17, 2022 (156)
102	EVA	ss5855412317	Oct 17, 2022 (156)
103	EVA	ss5884356149	Oct 17, 2022 (156)
104	EVA	ss5969178777	Oct 17, 2022 (156)
105	1000Genomes	NC_000006.11 - 72269242	Oct 12, 2018 (152)
106	1000Genomes_30x	NC_000006.12 - 71559539	Oct 17, 2022 (156)
107	The Avon Longitudinal Study of Parents and Children	NC_000006.11 - 72269242	Oct 12, 2018 (152)
108	Genetic variation in the Estonian population	NC_000006.11 - 72269242	Oct 12, 2018 (152)
109	The Danish reference pan genome	NC_000006.11 - 72269242	Apr 26, 2020 (154)
110	gnomAD - Genomes	NC_000006.12 - 71559539	Apr 26, 2021 (155)
111	Genome of the Netherlands Release 5	NC_000006.11 - 72269242	Apr 26, 2020 (154)
112	HGDP-CEPH-db Supplement 1	NC_000006.10 - 72325963	Apr 26, 2020 (154)
113	HapMap	NC_000006.12 - 71559539	Apr 26, 2020 (154)
114	KOREAN population from KRGDB	NC_000006.11 - 72269242	Apr 26, 2020 (154)
115	Northern Sweden	NC_000006.11 - 72269242	Jul 13, 2019 (153)
116	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000006.11 - 72269242	Apr 26, 2021 (155)
117	Qatari	NC_000006.11 - 72269242	Apr 26, 2020 (154)
118	SGDP_PRJ	NC_000006.11 - 72269242	Apr 26, 2020 (154)
119	Siberian	NC_000006.11 - 72269242	Apr 26, 2020 (154)
120	8.3KJPN	NC_000006.11 - 72269242	Apr 26, 2021 (155)
121	14KJPN	NC_000006.12 - 71559539	Oct 17, 2022 (156)
122	TopMed	NC_000006.12 - 71559539	Apr 26, 2021 (155)
123	UK 10K study - Twins	NC_000006.11 - 72269242	Oct 12, 2018 (152)
124	A Vietnamese Genetic Variation Database	NC_000006.11 - 72269242	Jul 13, 2019 (153)
125	ALFA	NC_000006.12 - 71559539	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)
rs59353344	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss77596396, ss3639318997, ss3639685620	NC_000006.9:72325962:C:T	NC_000006.12:71559538:C:T	(self)
515906, ss93489554, ss110318821, ss114545961, ss163699056, ss166863346, ss202003811, ss207631819, ss278861261, ss285436296, ss293633140, ss485279311, ss825627109, ss1592621517, ss1712872059, ss2635158490, ss3643577718, ss3847838014	NC_000006.10:72325962:C:T	NC_000006.12:71559538:C:T	(self)
32489973, 18101840, 12913108, 7897276, 8064590, 18915202, 6915366, 455773, 8377582, 16888211, 4518000, 36094098, 18101840, 4021191, ss222464252, ss233529276, ss240573520, ss483542772, ss535749903, ss559284499, ss653240925, ss780316908, ss782214924, ss833178843, ss835803977, ss983079227, ss1073720859, ss1320681757, ss1430776318, ss1581732337, ss1615854222, ss1658848255, ss1804497061, ss1926335652, ss1970431307, ss2023809854, ss2152001646, ss2626399403, ss2634466886, ss2707610375, ss2840535822, ss2999305705, ss3347043075, ss3629574575, ss3632382437, ss3638637153, ss3642496659, ss3667174860, ss3733630501, ss3765185405, ss3785513035, ss3790858172, ss3795737229, ss3829996808, ss3838478254, ss3864871231, ss3911737808, ss3985229846, ss4017281289, ss5178124791, ss5315164532, ss5508553129, ss5640684222, ss5842445558, ss5969178777	NC_000006.11:72269241:C:T	NC_000006.12:71559538:C:T	(self)
42655167, 229311196, 3161272, 50328038, 545199078, 14089248601, ss2285023701, ss3025698149, ss3648383981, ss3717487742, ss3808333973, ss3843925304, ss4707821520, ss5268943203, ss5466538117, ss5555129232, ss5716490934, ss5807602987, ss5855412317, ss5884356149	NC_000006.12:71559538:C:T	NC_000006.12:71559538:C:T	(self)
ss13053140, ss19673789, ss22370036	NT_007299.12:10089414:C:T	NC_000006.12:71559538:C:T	(self)
ss66630212, ss67918053, ss68042970, ss71607624, ss75457832, ss79296591, ss84819428, ss98259562, ss98508493, ss122993136, ss144044472, ss154494086, ss159668098, ss172464922, ss174842680, ss410867567	NT_007299.13:10389075:C:T	NC_000006.12:71559538: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 rs9442679

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

rs9442679