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dbSNP Short Genetic Variations

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.

rs6702619

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:99580690 (GRCh38.p13) 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>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.329835 (87304/264690, TOPMED)
G=0.456649 (70386/154136, ALFA)
G=0.357532 (50063/140024, GnomAD) (+ 17 more)
G=0.03323 (557/16760, 8.3KJPN)
G=0.2159 (1081/5008, 1000G)
G=0.4967 (2225/4480, Estonian)
G=0.4953 (1909/3854, ALSPAC)
T=0.4954 (1837/3708, TWINSUK)
G=0.0322 (94/2922, KOREAN)
G=0.1892 (358/1892, HapMap)
G=0.0295 (54/1832, Korea1K)
G=0.492 (491/998, GoNL)
G=0.262 (164/626, Chileans)
G=0.487 (292/600, NorthernSweden)
G=0.218 (47/216, Qatari)
G=0.075 (16/214, Vietnamese)
T=0.364 (59/162, SGDP_PRJ)
T=0.38 (36/96, Ancient Sardinia)
G=0.42 (17/40, GENOME_DK)
T=0.43 (13/30, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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.p13 chr 1 NC_000001.11:g.99580690T>G
GRCh37.p13 chr 1 NC_000001.10:g.100046246T>G
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

ALFA Allele Frequency (New)
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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 154136 T=0.543351 G=0.456649
European Sub 129660 T=0.504728 G=0.495272
African Sub 7356 T=0.8626 G=0.1374
African Others Sub 254 T=0.937 G=0.063
African American Sub 7102 T=0.8599 G=0.1401
Asian Sub 678 T=0.945 G=0.055
East Asian Sub 514 T=0.955 G=0.045
Other Asian Sub 164 T=0.915 G=0.085
Latin American 1 Sub 898 T=0.653 G=0.347
Latin American 2 Sub 8490 T=0.7576 G=0.2424
South Asian Sub 196 T=0.791 G=0.209
Other Sub 6858 T=0.6048 G=0.3952


Help

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 264690 T=0.670165 G=0.329835
gnomAD - Genomes Global Study-wide 140024 T=0.642468 G=0.357532
gnomAD - Genomes European Sub 75812 T=0.50025 G=0.49975
gnomAD - Genomes African Sub 41996 T=0.86387 G=0.13613
gnomAD - Genomes American Sub 13630 T=0.69765 G=0.30235
gnomAD - Genomes Ashkenazi Jewish Sub 3316 T=0.5820 G=0.4180
gnomAD - Genomes East Asian Sub 3116 T=0.9483 G=0.0517
gnomAD - Genomes Other Sub 2154 T=0.6328 G=0.3672
8.3KJPN JAPANESE Study-wide 16760 T=0.96677 G=0.03323
1000Genomes Global Study-wide 5008 T=0.7841 G=0.2159
1000Genomes African Sub 1322 T=0.9198 G=0.0802
1000Genomes East Asian Sub 1008 T=0.9315 G=0.0685
1000Genomes Europe Sub 1006 T=0.5229 G=0.4771
1000Genomes South Asian Sub 978 T=0.745 G=0.255
1000Genomes American Sub 694 T=0.745 G=0.255
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.5033 G=0.4967
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.5047 G=0.4953
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.4954 G=0.5046
KOREAN population from KRGDB KOREAN Study-wide 2922 T=0.9678 G=0.0322
HapMap Global Study-wide 1892 T=0.8108 G=0.1892
HapMap American Sub 770 T=0.709 G=0.291
HapMap African Sub 692 T=0.926 G=0.074
HapMap Asian Sub 254 T=0.957 G=0.043
HapMap Europe Sub 176 T=0.591 G=0.409
Korean Genome Project KOREAN Study-wide 1832 T=0.9705 G=0.0295
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.508 G=0.492
Chileans Chilean Study-wide 626 T=0.738 G=0.262
Northern Sweden ACPOP Study-wide 600 T=0.513 G=0.487
Qatari Global Study-wide 216 T=0.782 G=0.218
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.925 G=0.075
SGDP_PRJ Global Study-wide 162 T=0.364 G=0.636
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 96 T=0.38 G=0.62
The Danish reference pan genome Danish Study-wide 40 T=0.57 G=0.42
Siberian Global Study-wide 30 T=0.43 G=0.57
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 T= G
GRCh38.p13 chr 1 NC_000001.11:g.99580690= NC_000001.11:g.99580690T>G
GRCh37.p13 chr 1 NC_000001.10:g.100046246= NC_000001.10:g.100046246T>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#.

96 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 BCM_SSAHASNP ss9902864 Jul 11, 2003 (116)
2 PERLEGEN ss14883015 Dec 05, 2003 (119)
3 SSAHASNP ss20590019 Apr 05, 2004 (121)
4 PERLEGEN ss24244016 Sep 20, 2004 (123)
5 ABI ss44059806 Mar 13, 2006 (126)
6 ILLUMINA ss65771176 Oct 15, 2006 (127)
7 AFFY ss65921719 Nov 30, 2006 (127)
8 AFFY ss66312096 Nov 30, 2006 (127)
9 PERLEGEN ss68775403 May 17, 2007 (127)
10 ILLUMINA ss75109786 Dec 07, 2007 (129)
11 AFFY ss75993009 Dec 07, 2007 (129)
12 KRIBB_YJKIM ss82292670 Dec 14, 2007 (130)
13 BCMHGSC_JDW ss87656458 Mar 23, 2008 (129)
14 HUMANGENOME_JCVI ss97961320 Feb 06, 2009 (130)
15 1000GENOMES ss108453549 Jan 23, 2009 (130)
16 ILLUMINA-UK ss118919103 Feb 15, 2009 (130)
17 ENSEMBL ss138045082 Dec 01, 2009 (131)
18 ENSEMBL ss138842542 Dec 01, 2009 (131)
19 GMI ss155415405 Dec 01, 2009 (131)
20 ILLUMINA ss160799863 Dec 01, 2009 (131)
21 COMPLETE_GENOMICS ss164868875 Jul 04, 2010 (132)
22 COMPLETE_GENOMICS ss166904548 Jul 04, 2010 (132)
23 AFFY ss170131053 Jul 04, 2010 (132)
24 ILLUMINA ss174076028 Jul 04, 2010 (132)
25 BCM-HGSC-SUB ss205325675 Jul 04, 2010 (132)
26 1000GENOMES ss218548619 Jul 14, 2010 (132)
27 1000GENOMES ss230656717 Jul 14, 2010 (132)
28 1000GENOMES ss238323685 Jul 15, 2010 (132)
29 BL ss253315892 May 09, 2011 (134)
30 GMI ss275945302 May 04, 2012 (137)
31 PJP ss290580479 May 09, 2011 (134)
32 ILLUMINA ss481323330 May 04, 2012 (137)
33 ILLUMINA ss481348516 May 04, 2012 (137)
34 ILLUMINA ss482329815 Sep 08, 2015 (146)
35 ILLUMINA ss485456794 May 04, 2012 (137)
36 ILLUMINA ss537380716 Sep 08, 2015 (146)
37 TISHKOFF ss554480482 Apr 25, 2013 (138)
38 SSMP ss648253902 Apr 25, 2013 (138)
39 ILLUMINA ss778948445 Sep 08, 2015 (146)
40 ILLUMINA ss783173875 Sep 08, 2015 (146)
41 ILLUMINA ss784129342 Sep 08, 2015 (146)
42 ILLUMINA ss832433442 Sep 08, 2015 (146)
43 ILLUMINA ss834410264 Sep 08, 2015 (146)
44 EVA-GONL ss975482969 Aug 21, 2014 (142)
45 JMKIDD_LAB ss1068127659 Aug 21, 2014 (142)
46 1000GENOMES ss1292107584 Aug 21, 2014 (142)
47 DDI ss1425910977 Apr 01, 2015 (144)
48 EVA_GENOME_DK ss1574271531 Apr 01, 2015 (144)
49 EVA_DECODE ss1584861271 Apr 01, 2015 (144)
50 EVA_UK10K_ALSPAC ss1600816883 Apr 01, 2015 (144)
51 EVA_UK10K_TWINSUK ss1643810916 Apr 01, 2015 (144)
52 EVA_SVP ss1712357142 Apr 01, 2015 (144)
53 ILLUMINA ss1751859110 Sep 08, 2015 (146)
54 WEILL_CORNELL_DGM ss1918682575 Feb 12, 2016 (147)
55 JJLAB ss2019862768 Sep 14, 2016 (149)
56 USC_VALOUEV ss2147881474 Dec 20, 2016 (150)
57 HUMAN_LONGEVITY ss2165030960 Dec 20, 2016 (150)
58 TOPMED ss2327381769 Dec 20, 2016 (150)
59 ILLUMINA ss2632553618 Nov 08, 2017 (151)
60 GRF ss2697808808 Nov 08, 2017 (151)
61 GNOMAD ss2758637576 Nov 08, 2017 (151)
62 SWEGEN ss2987305660 Nov 08, 2017 (151)
63 BIOINF_KMB_FNS_UNIBA ss3023694976 Nov 08, 2017 (151)
64 TOPMED ss3084649611 Nov 08, 2017 (151)
65 CSHL ss3343595905 Nov 08, 2017 (151)
66 ILLUMINA ss3626165278 Oct 11, 2018 (152)
67 ILLUMINA ss3630587792 Oct 11, 2018 (152)
68 ILLUMINA ss3632903280 Oct 11, 2018 (152)
69 ILLUMINA ss3633598278 Oct 11, 2018 (152)
70 ILLUMINA ss3634339252 Oct 11, 2018 (152)
71 ILLUMINA ss3635291889 Oct 11, 2018 (152)
72 ILLUMINA ss3636016808 Oct 11, 2018 (152)
73 ILLUMINA ss3637042345 Oct 11, 2018 (152)
74 ILLUMINA ss3637775450 Oct 11, 2018 (152)
75 ILLUMINA ss3640046612 Oct 11, 2018 (152)
76 ILLUMINA ss3640984523 Oct 11, 2018 (152)
77 ILLUMINA ss3641278511 Oct 11, 2018 (152)
78 ILLUMINA ss3642785635 Oct 11, 2018 (152)
79 URBANLAB ss3646731430 Oct 11, 2018 (152)
80 EGCUT_WGS ss3655390736 Jul 12, 2019 (153)
81 EVA_DECODE ss3687367117 Jul 12, 2019 (153)
82 ACPOP ss3727314052 Jul 12, 2019 (153)
83 ILLUMINA ss3744640221 Jul 12, 2019 (153)
84 EVA ss3746574087 Jul 12, 2019 (153)
85 ILLUMINA ss3772141458 Jul 12, 2019 (153)
86 KHV_HUMAN_GENOMES ss3799574865 Jul 12, 2019 (153)
87 EVA ss3826326553 Apr 25, 2020 (154)
88 EVA ss3836553556 Apr 25, 2020 (154)
89 EVA ss3841961553 Apr 25, 2020 (154)
90 SGDP_PRJ ss3849477554 Apr 25, 2020 (154)
91 KRGDB ss3894555566 Apr 25, 2020 (154)
92 KOGIC ss3945091313 Apr 25, 2020 (154)
93 EVA ss3984814965 Apr 25, 2021 (155)
94 EVA ss4016927690 Apr 25, 2021 (155)
95 TOPMED ss4460697331 Apr 25, 2021 (155)
96 TOMMO_GENOMICS ss5145313210 Apr 25, 2021 (155)
97 1000Genomes NC_000001.10 - 100046246 Oct 11, 2018 (152)
98 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 100046246 Oct 11, 2018 (152)
99 Chileans NC_000001.10 - 100046246 Apr 25, 2020 (154)
100 Genetic variation in the Estonian population NC_000001.10 - 100046246 Oct 11, 2018 (152)
101 The Danish reference pan genome NC_000001.10 - 100046246 Apr 25, 2020 (154)
102 gnomAD - Genomes NC_000001.11 - 99580690 Apr 25, 2021 (155)
103 Genome of the Netherlands Release 5 NC_000001.10 - 100046246 Apr 25, 2020 (154)
104 HapMap NC_000001.11 - 99580690 Apr 25, 2020 (154)
105 KOREAN population from KRGDB NC_000001.10 - 100046246 Apr 25, 2020 (154)
106 Korean Genome Project NC_000001.11 - 99580690 Apr 25, 2020 (154)
107 Northern Sweden NC_000001.10 - 100046246 Jul 12, 2019 (153)
108 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 100046246 Apr 25, 2021 (155)
109 Qatari NC_000001.10 - 100046246 Apr 25, 2020 (154)
110 SGDP_PRJ NC_000001.10 - 100046246 Apr 25, 2020 (154)
111 Siberian NC_000001.10 - 100046246 Apr 25, 2020 (154)
112 8.3KJPN NC_000001.10 - 100046246 Apr 25, 2021 (155)
113 TopMed NC_000001.11 - 99580690 Apr 25, 2021 (155)
114 UK 10K study - Twins NC_000001.10 - 100046246 Oct 11, 2018 (152)
115 A Vietnamese Genetic Variation Database NC_000001.10 - 100046246 Jul 12, 2019 (153)
116 ALFA NC_000001.11 - 99580690 Apr 25, 2021 (155)
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)
rs17404809 Oct 07, 2004 (123)
rs57875354 Feb 27, 2009 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss87656458, ss108453549, ss118919103, ss164868875, ss166904548, ss205325675, ss253315892, ss275945302, ss290580479, ss481323330, ss1584861271, ss1712357142, ss3642785635 NC_000001.9:99818833:T:G NC_000001.11:99580689:T:G (self)
2871153, 1583813, 16659, 1128984, 1628939, 687066, 1732960, 598917, 40892, 724505, 1494534, 397828, 3282517, 1583813, 341163, ss218548619, ss230656717, ss238323685, ss481348516, ss482329815, ss485456794, ss537380716, ss554480482, ss648253902, ss778948445, ss783173875, ss784129342, ss832433442, ss834410264, ss975482969, ss1068127659, ss1292107584, ss1425910977, ss1574271531, ss1600816883, ss1643810916, ss1751859110, ss1918682575, ss2019862768, ss2147881474, ss2327381769, ss2632553618, ss2697808808, ss2758637576, ss2987305660, ss3343595905, ss3626165278, ss3630587792, ss3632903280, ss3633598278, ss3634339252, ss3635291889, ss3636016808, ss3637042345, ss3637775450, ss3640046612, ss3640984523, ss3641278511, ss3655390736, ss3727314052, ss3744640221, ss3746574087, ss3772141458, ss3826326553, ss3836553556, ss3849477554, ss3894555566, ss3984814965, ss4016927690, ss5145313210 NC_000001.10:100046245:T:G NC_000001.11:99580689:T:G (self)
20296553, 136549, 1469314, 15307051, 24303666, 10744201158, ss2165030960, ss3023694976, ss3084649611, ss3646731430, ss3687367117, ss3799574865, ss3841961553, ss3945091313, ss4460697331 NC_000001.11:99580689:T:G NC_000001.11:99580689:T:G (self)
ss9902864 NT_028050.12:919916:T:G NC_000001.11:99580689:T:G (self)
ss20590019 NT_028050.13:8235189:T:G NC_000001.11:99580689:T:G (self)
ss14883015, ss24244016, ss44059806, ss65771176, ss65921719, ss66312096, ss68775403, ss75109786, ss75993009, ss82292670, ss97961320, ss138045082, ss138842542, ss155415405, ss160799863, ss170131053, ss174076028 NT_032977.9:70018163:T:G NC_000001.11:99580689:T: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 rs6702619
PMID Title Author Year Journal
22532847 Pooled sample-based GWAS: a cost-effective alternative for identifying colorectal and prostate cancer risk variants in the Polish population. Gaj P et al. 2012 PloS one
31531420 Functional analyses of a low-penetrance risk variant rs6702619/1p21.2 associating with colorectal cancer in Polish population. Statkiewicz M et al. 2019 Acta biochimica Polonica
Help

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.

Software version is: 2.0.1.post596+ae089ad