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dbSNP Short Genetic Variations

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.

rs6689169

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr1:240775117 (GRCh38.p12) 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
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.18215 (22872/125568, TOPMED)
G=0.1710 (5364/31360, GnomAD)
G=0.173 (866/5008, 1000G) (+ 5 more)
G=0.098 (439/4480, Estonian)
G=0.119 (459/3854, ALSPAC)
G=0.126 (468/3708, TWINSUK)
G=0.09 (56/600, NorthernSweden)
G=0.13 (28/214, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
RGS7 : 500B Downstream Variant
Publications
2 citations
Genomic View
See rs on genome
Help

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.p12 chr 1 NC_000001.11:g.240775117A>G
GRCh37.p13 chr 1 NC_000001.10:g.240938417A>G
Gene: RGS7, regulator of G protein signaling 7 (minus strand) : 500B Downstream Variant
Molecule type Change Amino acid[Codon] SO Term
RGS7 transcript variant 2 NM_001282773.2:c. N/A Downstream Transcript Variant
RGS7 transcript variant 3 NM_001282775.2:c. N/A Downstream Transcript Variant
RGS7 transcript variant 4 NM_001282778.2:c. N/A Downstream Transcript Variant
RGS7 transcript variant 5 NM_001350113.1:c. N/A Downstream Transcript Variant
RGS7 transcript variant 6 NM_001350114.1:c. N/A Downstream Transcript Variant
RGS7 transcript variant 7 NM_001350115.1:c. N/A Downstream Transcript Variant
RGS7 transcript variant 8 NM_001350116.1:c. N/A Downstream Transcript Variant
RGS7 transcript variant 9 NM_001364886.1:c. N/A Downstream Transcript Variant
RGS7 transcript variant 1 NM_002924.6:c. N/A Downstream Transcript Variant
RGS7 transcript variant X4 XM_006711800.4:c. N/A Downstream Transcript Variant
RGS7 transcript variant X5 XM_011544246.3:c. N/A Downstream Transcript Variant
RGS7 transcript variant X6 XM_011544247.3:c. N/A Downstream Transcript Variant
RGS7 transcript variant X2 XM_017002001.2:c. N/A Downstream Transcript Variant
RGS7 transcript variant X3 XM_017002002.2:c. N/A Downstream Transcript Variant
RGS7 transcript variant X7 XM_017002003.2:c. N/A Downstream Transcript Variant
RGS7 transcript variant X8 XM_017002004.2:c. N/A Downstream Transcript Variant
RGS7 transcript variant X9 XM_017002005.2:c. N/A Downstream Transcript Variant
RGS7 transcript variant X10 XM_017002009.1:c. N/A Downstream Transcript Variant
RGS7 transcript variant X11 XM_017002011.2:c. N/A Downstream Transcript Variant
RGS7 transcript variant X12 XM_017002012.2:c. N/A Downstream Transcript Variant
RGS7 transcript variant X13 XM_017002013.1:c. N/A Downstream Transcript Variant
Help

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
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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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 125568 A=0.81785 G=0.18215
gnomAD - Genomes Global Study-wide 31360 A=0.8290 G=0.1710
gnomAD - Genomes European Sub 18898 A=0.8901 G=0.1099
gnomAD - Genomes African Sub 8680 A=0.674 G=0.326
gnomAD - Genomes East Asian Sub 1558 A=0.858 G=0.142
gnomAD - Genomes Other Sub 1088 A=0.898 G=0.102
gnomAD - Genomes American Sub 846 A=0.90 G=0.10
gnomAD - Genomes Ashkenazi Jewish Sub 290 A=0.87 G=0.13
1000Genomes Global Study-wide 5008 A=0.827 G=0.173
1000Genomes African Sub 1322 A=0.642 G=0.358
1000Genomes East Asian Sub 1008 A=0.874 G=0.126
1000Genomes Europe Sub 1006 A=0.887 G=0.113
1000Genomes South Asian Sub 978 A=0.91 G=0.09
1000Genomes American Sub 694 A=0.91 G=0.09
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.902 G=0.098
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.881 G=0.119
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.874 G=0.126
Northern Sweden ACPOP Study-wide 600 A=0.91 G=0.09
A Vietnamese Genetic Variation Database Global Study-wide 214 A=0.87 G=0.13
Help

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 Note
GRCh38.p12 chr 1 NC_000001.11:g.240775117= NC_000001.11:g.24077511...

NC_000001.11:g.240775117A>G

GRCh37.p13 chr 1 NC_000001.10:g.240938417= NC_000001.10:g.24093841...

NC_000001.10:g.240938417A>G

Help

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#.

67 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 BCM_SSAHASNP ss9875090 Jul 11, 2003 (116)
2 PERLEGEN ss23213307 Sep 20, 2004 (123)
3 ILLUMINA ss66688267 Nov 29, 2006 (127)
4 ILLUMINA ss67485090 Nov 29, 2006 (127)
5 ILLUMINA ss67842905 Nov 29, 2006 (127)
6 PERLEGEN ss68798924 May 16, 2007 (127)
7 ILLUMINA ss70879759 May 23, 2008 (130)
8 ILLUMINA ss71470217 May 16, 2007 (127)
9 ILLUMINA ss75567587 Dec 07, 2007 (129)
10 ILLUMINA ss79229835 Dec 14, 2007 (130)
11 KRIBB_YJKIM ss84524092 Dec 14, 2007 (130)
12 BGI ss102837898 Dec 01, 2009 (131)
13 ILLUMINA-UK ss119270518 Feb 15, 2009 (130)
14 ILLUMINA ss122594359 Dec 01, 2009 (131)
15 ENSEMBL ss143790679 Dec 01, 2009 (131)
16 ILLUMINA ss154375423 Dec 01, 2009 (131)
17 ILLUMINA ss159551317 Dec 01, 2009 (131)
18 ILLUMINA ss172171877 Jul 04, 2010 (132)
19 ILLUMINA ss174070147 Jul 04, 2010 (132)
20 BUSHMAN ss199835317 Jul 04, 2010 (132)
21 1000GENOMES ss218977107 Jul 14, 2010 (132)
22 1000GENOMES ss230973964 Jul 14, 2010 (132)
23 1000GENOMES ss238573880 Jul 15, 2010 (132)
24 GMI ss276288331 May 04, 2012 (137)
25 ILLUMINA ss537378826 Sep 08, 2015 (146)
26 TISHKOFF ss555252219 Apr 25, 2013 (138)
27 SSMP ss648826308 Apr 25, 2013 (138)
28 ILLUMINA ss825560353 Apr 01, 2015 (144)
29 ILLUMINA ss833062490 Aug 21, 2014 (142)
30 ILLUMINA ss833653318 Aug 21, 2014 (142)
31 EVA-GONL ss976329291 Aug 21, 2014 (142)
32 JMKIDD_LAB ss1068741570 Aug 21, 2014 (142)
33 1000GENOMES ss1295330580 Aug 21, 2014 (142)
34 DDI ss1426166742 Apr 01, 2015 (144)
35 EVA_GENOME_DK ss1574798332 Apr 01, 2015 (144)
36 EVA_DECODE ss1585733682 Apr 01, 2015 (144)
37 EVA_UK10K_ALSPAC ss1602505545 Apr 01, 2015 (144)
38 EVA_UK10K_TWINSUK ss1645499578 Apr 01, 2015 (144)
39 EVA_SVP ss1712419768 Apr 01, 2015 (144)
40 HAMMER_LAB ss1795994173 Sep 08, 2015 (146)
41 WEILL_CORNELL_DGM ss1919550980 Feb 12, 2016 (147)
42 GENOMED ss1967017550 Jul 19, 2016 (147)
43 JJLAB ss2020303070 Sep 14, 2016 (149)
44 USC_VALOUEV ss2148341013 Nov 08, 2017 (151)
45 HUMAN_LONGEVITY ss2171487067 Dec 20, 2016 (150)
46 TOPMED ss2334139456 Dec 20, 2016 (150)
47 SYSTEMSBIOZJU ss2624664897 Nov 08, 2017 (151)
48 GRF ss2698344461 Nov 08, 2017 (151)
49 GNOMAD ss2768126108 Nov 08, 2017 (151)
50 SWEGEN ss2988734507 Nov 08, 2017 (151)
51 ILLUMINA ss3021198133 Nov 08, 2017 (151)
52 BIOINF_KMB_FNS_UNIBA ss3023913882 Nov 08, 2017 (151)
53 TOPMED ss3107763951 Nov 08, 2017 (151)
54 CSHL ss3343995519 Nov 08, 2017 (151)
55 ILLUMINA ss3626349812 Oct 11, 2018 (152)
56 ILLUMINA ss3637824694 Oct 11, 2018 (152)
57 ILLUMINA ss3638927502 Oct 11, 2018 (152)
58 ILLUMINA ss3639462865 Oct 11, 2018 (152)
59 ILLUMINA ss3642830150 Oct 11, 2018 (152)
60 URBANLAB ss3646926104 Oct 11, 2018 (152)
61 ILLUMINA ss3651544246 Oct 11, 2018 (152)
62 EGCUT_WGS ss3656695642 Jul 12, 2019 (153)
63 EVA_DECODE ss3688972829 Jul 12, 2019 (153)
64 ILLUMINA ss3725121750 Jul 12, 2019 (153)
65 ACPOP ss3728017272 Jul 12, 2019 (153)
66 EVA ss3747551363 Jul 12, 2019 (153)
67 KHV_HUMAN_GENOMES ss3800554805 Jul 12, 2019 (153)
68 1000Genomes NC_000001.10 - 240938417 Oct 11, 2018 (152)
69 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 240938417 Oct 11, 2018 (152)
70 Genetic variation in the Estonian population NC_000001.10 - 240938417 Oct 11, 2018 (152)
71 gnomAD - Genomes NC_000001.10 - 240938417 Jul 12, 2019 (153)
72 Northern Sweden NC_000001.10 - 240938417 Jul 12, 2019 (153)
73 TopMed NC_000001.11 - 240775117 Oct 11, 2018 (152)
74 UK 10K study - Twins NC_000001.10 - 240938417 Oct 11, 2018 (152)
75 A Vietnamese Genetic Variation Database NC_000001.10 - 240938417 Jul 12, 2019 (153)
Help

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)
rs56728136 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss3638927502, ss3639462865 NC_000001.8:237264457:A:G NC_000001.11:240775116:A:G (self)
ss119270518, ss199835317, ss276288331, ss825560353, ss1585733682, ss1712419768, ss3642830150 NC_000001.9:239005039:A:G NC_000001.11:240775116:A:G (self)
6210582, 3441516, 2433890, 16950460, 1302137, 3441516, 750543, ss218977107, ss230973964, ss238573880, ss537378826, ss555252219, ss648826308, ss833062490, ss833653318, ss976329291, ss1068741570, ss1295330580, ss1426166742, ss1574798332, ss1602505545, ss1645499578, ss1795994173, ss1919550980, ss1967017550, ss2020303070, ss2148341013, ss2334139456, ss2624664897, ss2698344461, ss2768126108, ss2988734507, ss3021198133, ss3343995519, ss3626349812, ss3637824694, ss3651544246, ss3656695642, ss3728017272, ss3747551363 NC_000001.10:240938416:A:G NC_000001.11:240775116:A:G (self)
33349985, ss2171487067, ss3023913882, ss3107763951, ss3646926104, ss3688972829, ss3725121750, ss3800554805 NC_000001.11:240775116:A:G NC_000001.11:240775116:A:G (self)
ss9875090 NT_004836.14:5681775:A:G NC_000001.11:240775116:A:G (self)
ss23213307, ss66688267, ss67485090, ss67842905, ss68798924, ss70879759, ss71470217, ss75567587, ss79229835, ss84524092, ss102837898, ss122594359, ss143790679, ss154375423, ss159551317, ss172171877, ss174070147 NT_167186.1:34456195:A:G NC_000001.11:240775116:A:G (self)
Help

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

2 citations for rs6689169
PMID Title Author Year Journal
20627871 Genetic variations in regulator of G-protein signaling genes as susceptibility loci for second primary tumor/recurrence in head and neck squamous cell carcinoma. Wang J et al. 2010 Carcinogenesis
21698121 Genetic variations in the regulator of G-protein signaling genes are associated with survival in late-stage non-small cell lung cancer. Dai J et al. 2011 PloS one

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.

Software version is: 2.0.1.post270+ab078da