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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.

rs3095649

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr16:48859502 (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>C / A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.194318 (51434/264690, TOPMED)
A=0.192119 (26919/140116, GnomAD)
A=0.03787 (1070/28258, 14KJPN) (+ 16 more)
A=0.03598 (603/16760, 8.3KJPN)
A=0.18866 (3151/16702, ALFA)
A=0.1682 (1077/6404, 1000G_30x)
A=0.1665 (834/5008, 1000G)
A=0.1752 (785/4480, Estonian)
A=0.1754 (676/3854, ALSPAC)
A=0.1907 (707/3708, TWINSUK)
A=0.0498 (146/2930, KOREAN)
A=0.0644 (118/1832, Korea1K)
A=0.158 (158/998, GoNL)
A=0.160 (96/600, NorthernSweden)
A=0.100 (54/538, SGDP_PRJ)
A=0.213 (46/216, Qatari)
A=0.023 (5/214, Vietnamese)
A=0.12 (7/56, Siberian)
A=0.17 (7/40, GENOME_DK)
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 16702 A=0.18866 T=0.81134
European Sub 12214 A=0.18765 T=0.81235
African Sub 2864 A=0.2078 T=0.7922
African Others Sub 108 A=0.204 T=0.796
African American Sub 2756 A=0.2079 T=0.7921
Asian Sub 108 A=0.028 T=0.972
East Asian Sub 84 A=0.02 T=0.98
Other Asian Sub 24 A=0.04 T=0.96
Latin American 1 Sub 146 A=0.205 T=0.795
Latin American 2 Sub 610 A=0.157 T=0.843
South Asian Sub 94 A=0.22 T=0.78
Other Sub 666 A=0.171 T=0.829


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 A=0.194318 T=0.805682
gnomAD - Genomes Global Study-wide 140116 A=0.192119 T=0.807881
gnomAD - Genomes European Sub 75896 A=0.18122 T=0.81878
gnomAD - Genomes African Sub 41954 A=0.22181 T=0.77819
gnomAD - Genomes American Sub 13654 A=0.17306 T=0.82694
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=0.2912 T=0.7088
gnomAD - Genomes East Asian Sub 3134 A=0.0284 T=0.9716
gnomAD - Genomes Other Sub 2154 A=0.2038 T=0.7962
14KJPN JAPANESE Study-wide 28258 A=0.03787 T=0.96213
8.3KJPN JAPANESE Study-wide 16760 A=0.03598 T=0.96402
Allele Frequency Aggregator Total Global 16702 A=0.18866 T=0.81134
Allele Frequency Aggregator European Sub 12214 A=0.18765 T=0.81235
Allele Frequency Aggregator African Sub 2864 A=0.2078 T=0.7922
Allele Frequency Aggregator Other Sub 666 A=0.171 T=0.829
Allele Frequency Aggregator Latin American 2 Sub 610 A=0.157 T=0.843
Allele Frequency Aggregator Latin American 1 Sub 146 A=0.205 T=0.795
Allele Frequency Aggregator Asian Sub 108 A=0.028 T=0.972
Allele Frequency Aggregator South Asian Sub 94 A=0.22 T=0.78
1000Genomes_30x Global Study-wide 6404 A=0.1682 T=0.8318
1000Genomes_30x African Sub 1786 A=0.2284 T=0.7716
1000Genomes_30x Europe Sub 1266 A=0.2133 T=0.7867
1000Genomes_30x South Asian Sub 1202 A=0.1855 T=0.8145
1000Genomes_30x East Asian Sub 1170 A=0.0274 T=0.9726
1000Genomes_30x American Sub 980 A=0.147 T=0.853
1000Genomes Global Study-wide 5008 A=0.1665 T=0.8335
1000Genomes African Sub 1322 A=0.2337 T=0.7663
1000Genomes East Asian Sub 1008 A=0.0298 T=0.9702
1000Genomes Europe Sub 1006 A=0.2008 T=0.7992
1000Genomes South Asian Sub 978 A=0.191 T=0.809
1000Genomes American Sub 694 A=0.153 T=0.847
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.1752 T=0.8248
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.1754 T=0.8246
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.1907 T=0.8093
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.0498 C=0.0000, G=0.0000, T=0.9502
Korean Genome Project KOREAN Study-wide 1832 A=0.0644 T=0.9356
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.158 T=0.842
Northern Sweden ACPOP Study-wide 600 A=0.160 T=0.840
SGDP_PRJ Global Study-wide 538 A=0.100 T=0.900
Qatari Global Study-wide 216 A=0.213 T=0.787
A Vietnamese Genetic Variation Database Global Study-wide 214 A=0.023 T=0.977
Siberian Global Study-wide 56 A=0.12 T=0.88
The Danish reference pan genome Danish Study-wide 40 A=0.17 T=0.82
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.p14 chr 16 NC_000016.10:g.48859502A>C
GRCh38.p14 chr 16 NC_000016.10:g.48859502A>G
GRCh38.p14 chr 16 NC_000016.10:g.48859502A>T
GRCh37.p13 chr 16 NC_000016.9:g.48893413A>C
GRCh37.p13 chr 16 NC_000016.9:g.48893413A>G
GRCh37.p13 chr 16 NC_000016.9:g.48893413A>T
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
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= C G T
GRCh38.p14 chr 16 NC_000016.10:g.48859502= NC_000016.10:g.48859502A>C NC_000016.10:g.48859502A>G NC_000016.10:g.48859502A>T
GRCh37.p13 chr 16 NC_000016.9:g.48893413= NC_000016.9:g.48893413A>C NC_000016.9:g.48893413A>G NC_000016.9:g.48893413A>T
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#.

79 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss4331360 Mar 26, 2002 (103)
2 WI_SSAHASNP ss6603471 Feb 20, 2003 (111)
3 BCM_SSAHASNP ss10831522 Jul 11, 2003 (116)
4 SSAHASNP ss21355948 Apr 05, 2004 (121)
5 PERLEGEN ss24504420 Sep 20, 2004 (123)
6 HGSV ss77396881 Dec 06, 2007 (129)
7 HGSV ss79688346 Dec 14, 2007 (130)
8 BCMHGSC_JDW ss90386052 Mar 24, 2008 (129)
9 HUMANGENOME_JCVI ss96635082 Feb 03, 2009 (130)
10 BGI ss106469959 Feb 03, 2009 (130)
11 1000GENOMES ss109307112 Jan 23, 2009 (130)
12 1000GENOMES ss115052757 Jan 25, 2009 (130)
13 ILLUMINA-UK ss118244205 Feb 14, 2009 (130)
14 ENSEMBL ss132502350 Dec 01, 2009 (131)
15 ENSEMBL ss136713201 Dec 01, 2009 (131)
16 GMI ss157326761 Dec 01, 2009 (131)
17 COMPLETE_GENOMICS ss168170830 Jul 04, 2010 (132)
18 COMPLETE_GENOMICS ss169658398 Jul 04, 2010 (132)
19 COMPLETE_GENOMICS ss171220581 Jul 04, 2010 (132)
20 BUSHMAN ss201664351 Jul 04, 2010 (132)
21 BCM-HGSC-SUB ss207461749 Jul 04, 2010 (132)
22 1000GENOMES ss227228189 Jul 14, 2010 (132)
23 1000GENOMES ss237015960 Jul 15, 2010 (132)
24 1000GENOMES ss243356642 Jul 15, 2010 (132)
25 BL ss255686371 May 09, 2011 (134)
26 GMI ss282523561 May 04, 2012 (137)
27 GMI ss287071500 Apr 25, 2013 (138)
28 PJP ss291839266 May 09, 2011 (134)
29 TISHKOFF ss564884440 Apr 25, 2013 (138)
30 SSMP ss660655865 Apr 25, 2013 (138)
31 EVA-GONL ss992464652 Aug 21, 2014 (142)
32 JMKIDD_LAB ss1080604107 Aug 21, 2014 (142)
33 1000GENOMES ss1356148339 Aug 21, 2014 (142)
34 DDI ss1427840325 Apr 01, 2015 (144)
35 EVA_GENOME_DK ss1577904313 Apr 01, 2015 (144)
36 EVA_UK10K_ALSPAC ss1634368324 Apr 01, 2015 (144)
37 EVA_UK10K_TWINSUK ss1677362357 Apr 01, 2015 (144)
38 EVA_DECODE ss1696497455 Apr 01, 2015 (144)
39 HAMMER_LAB ss1808503318 Sep 08, 2015 (146)
40 WEILL_CORNELL_DGM ss1935899841 Feb 12, 2016 (147)
41 GENOMED ss1968255881 Jul 19, 2016 (147)
42 JJLAB ss2028731689 Sep 14, 2016 (149)
43 USC_VALOUEV ss2157167089 Dec 20, 2016 (150)
44 HUMAN_LONGEVITY ss2211954501 Dec 20, 2016 (150)
45 SYSTEMSBIOZJU ss2628857823 Nov 08, 2017 (151)
46 GRF ss2701690008 Nov 08, 2017 (151)
47 GNOMAD ss2942750194 Nov 08, 2017 (151)
48 SWEGEN ss3014478112 Nov 08, 2017 (151)
49 BIOINF_KMB_FNS_UNIBA ss3028184696 Nov 08, 2017 (151)
50 CSHL ss3351441733 Nov 08, 2017 (151)
51 URBANLAB ss3650505840 Oct 12, 2018 (152)
52 EGCUT_WGS ss3681451266 Jul 13, 2019 (153)
53 EVA_DECODE ss3699216749 Jul 13, 2019 (153)
54 ACPOP ss3741491130 Jul 13, 2019 (153)
55 EVA ss3753906491 Jul 13, 2019 (153)
56 PACBIO ss3788033833 Jul 13, 2019 (153)
57 PACBIO ss3793017579 Jul 13, 2019 (153)
58 PACBIO ss3797902548 Jul 13, 2019 (153)
59 KHV_HUMAN_GENOMES ss3819197488 Jul 13, 2019 (153)
60 EVA ss3834558151 Apr 27, 2020 (154)
61 EVA ss3840884520 Apr 27, 2020 (154)
62 EVA ss3846376179 Apr 27, 2020 (154)
63 SGDP_PRJ ss3884389983 Apr 27, 2020 (154)
64 KRGDB ss3933870260 Apr 27, 2020 (154)
65 KOGIC ss3977543357 Apr 27, 2020 (154)
66 TOPMED ss5014554719 Apr 26, 2021 (155)
67 TOMMO_GENOMICS ss5219469731 Apr 26, 2021 (155)
68 1000G_HIGH_COVERAGE ss5300878180 Oct 17, 2022 (156)
69 EVA ss5423557552 Oct 17, 2022 (156)
70 HUGCELL_USP ss5494234328 Oct 17, 2022 (156)
71 EVA ss5511604039 Oct 17, 2022 (156)
72 1000G_HIGH_COVERAGE ss5603483997 Oct 17, 2022 (156)
73 SANFORD_IMAGENETICS ss5658858513 Oct 17, 2022 (156)
74 TOMMO_GENOMICS ss5774450776 Oct 17, 2022 (156)
75 YY_MCH ss5815953973 Oct 17, 2022 (156)
76 EVA ss5846377810 Oct 17, 2022 (156)
77 EVA ss5851556779 Oct 17, 2022 (156)
78 EVA ss5899000041 Oct 17, 2022 (156)
79 EVA ss5950244802 Oct 17, 2022 (156)
80 1000Genomes NC_000016.9 - 48893413 Oct 12, 2018 (152)
81 1000Genomes_30x NC_000016.10 - 48859502 Oct 17, 2022 (156)
82 The Avon Longitudinal Study of Parents and Children NC_000016.9 - 48893413 Oct 12, 2018 (152)
83 Genetic variation in the Estonian population NC_000016.9 - 48893413 Oct 12, 2018 (152)
84 The Danish reference pan genome NC_000016.9 - 48893413 Apr 27, 2020 (154)
85 gnomAD - Genomes NC_000016.10 - 48859502 Apr 26, 2021 (155)
86 Genome of the Netherlands Release 5 NC_000016.9 - 48893413 Apr 27, 2020 (154)
87 KOREAN population from KRGDB NC_000016.9 - 48893413 Apr 27, 2020 (154)
88 Korean Genome Project NC_000016.10 - 48859502 Apr 27, 2020 (154)
89 Northern Sweden NC_000016.9 - 48893413 Jul 13, 2019 (153)
90 Qatari NC_000016.9 - 48893413 Apr 27, 2020 (154)
91 SGDP_PRJ NC_000016.9 - 48893413 Apr 27, 2020 (154)
92 Siberian NC_000016.9 - 48893413 Apr 27, 2020 (154)
93 8.3KJPN NC_000016.9 - 48893413 Apr 26, 2021 (155)
94 14KJPN NC_000016.10 - 48859502 Oct 17, 2022 (156)
95 TopMed NC_000016.10 - 48859502 Apr 26, 2021 (155)
96 UK 10K study - Twins NC_000016.9 - 48893413 Oct 12, 2018 (152)
97 A Vietnamese Genetic Variation Database NC_000016.9 - 48893413 Jul 13, 2019 (153)
98 ALFA NC_000016.10 - 48859502 Apr 26, 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)
rs17829999 Oct 08, 2004 (123)
rs56988846 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
41047654, ss3933870260 NC_000016.9:48893412:A:C NC_000016.10:48859501:A:C (self)
41047654, ss3933870260 NC_000016.9:48893412:A:G NC_000016.10:48859501:A:G (self)
ss77396881, ss79688346, ss90386052, ss109307112, ss115052757, ss118244205, ss168170830, ss169658398, ss171220581, ss201664351, ss207461749, ss255686371, ss282523561, ss287071500, ss291839266, ss1696497455 NC_000016.8:47450913:A:T NC_000016.10:48859501:A:T (self)
69307699, 38439951, 27189514, 4117131, 17145346, 41047654, 14775995, 17941763, 36406963, 9683443, 77439038, 38439951, 8529484, ss227228189, ss237015960, ss243356642, ss564884440, ss660655865, ss992464652, ss1080604107, ss1356148339, ss1427840325, ss1577904313, ss1634368324, ss1677362357, ss1808503318, ss1935899841, ss1968255881, ss2028731689, ss2157167089, ss2628857823, ss2701690008, ss2942750194, ss3014478112, ss3351441733, ss3681451266, ss3741491130, ss3753906491, ss3788033833, ss3793017579, ss3797902548, ss3834558151, ss3840884520, ss3884389983, ss3933870260, ss5219469731, ss5423557552, ss5511604039, ss5658858513, ss5846377810, ss5950244802 NC_000016.9:48893412:A:T NC_000016.10:48859501:A:T (self)
91009932, 488901875, 33921358, 108287880, 230100380, 9240889710, ss2211954501, ss3028184696, ss3650505840, ss3699216749, ss3819197488, ss3846376179, ss3977543357, ss5014554719, ss5300878180, ss5494234328, ss5603483997, ss5774450776, ss5815953973, ss5851556779, ss5899000041 NC_000016.10:48859501:A:T NC_000016.10:48859501:A:T (self)
ss4331360, ss6603471, ss24504420, ss96635082, ss106469959, ss132502350, ss136713201, ss157326761 NT_010498.15:2507611:A:T NC_000016.10:48859501:A:T (self)
ss10831522 NT_010505.13:1001914:A:T NC_000016.10:48859501:A:T (self)
ss21355948 NT_010505.14:1001914:A:T NC_000016.10:48859501:A:T (self)
Help

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

No publications for rs3095649

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.post761+d5e8e07