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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.

rs11645428

Current Build 154

Released April 21, 2020

Organism
Homo sapiens
Position
chr16:81225291 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.247746 (31109/125568, TOPMED)
A=0.31892 (17077/53546, ALFA Project)
A=0.25421 (7967/31340, GnomAD) (+ 16 more)
A=0.1556 (779/5008, 1000G)
A=0.3355 (1503/4480, Estonian)
A=0.3272 (1261/3854, ALSPAC)
A=0.3285 (1218/3708, TWINSUK)
A=0.0003 (1/2922, KOREAN)
A=0.1838 (383/2084, HGDP_Stanford)
A=0.1576 (272/1726, HapMap)
A=0.2928 (332/1134, Daghestan)
A=0.373 (372/998, GoNL)
A=0.208 (130/626, Chileans)
A=0.333 (200/600, NorthernSweden)
A=0.315 (68/216, Qatari)
A=0.019 (4/214, Vietnamese)
G=0.443 (62/140, SGDP_PRJ)
A=0.23 (9/40, GENOME_DK)
G=0.2 (2/8, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
6 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 16 NC_000016.10:g.81225291G>A
GRCh37.p13 chr 16 NC_000016.9:g.81258896G>A
PKD1L2 RefSeqGene NG_033236.1:g.80C>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

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: 20200227123210
Population Group Sample Size Ref Allele Alt Allele
Total Global 53546 G=0.68108 A=0.31892
European Sub 42620 G=0.64418 A=0.35582
African Sub 2256 G=0.8799 A=0.1201
African Others Sub 58 G=0.95 A=0.05
African American Sub 2198 G=0.8781 A=0.1219
Asian Sub 128 G=0.992 A=0.008
East Asian Sub 84 G=1.00 A=0.00
Other Asian Sub 44 G=0.98 A=0.02
Latin American 1 Sub 166 G=0.663 A=0.337
Latin American 2 Sub 2242 G=0.7877 A=0.2123
South Asian Sub 4854 G=0.8317 A=0.1683
Other Sub 1280 G=0.7727 A=0.2273


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 125568 G=0.752254 A=0.247746
ALFA Total Global 53546 G=0.68108 A=0.31892
ALFA European Sub 42620 G=0.64418 A=0.35582
ALFA South Asian Sub 4854 G=0.8317 A=0.1683
ALFA African Sub 2256 G=0.8799 A=0.1201
ALFA Latin American 2 Sub 2242 G=0.7877 A=0.2123
ALFA Other Sub 1280 G=0.7727 A=0.2273
ALFA Latin American 1 Sub 166 G=0.663 A=0.337
ALFA Asian Sub 128 G=0.992 A=0.008
gnomAD - Genomes Global Study-wide 31340 G=0.74579 A=0.25421
gnomAD - Genomes European Sub 18866 G=0.66299 A=0.33701
gnomAD - Genomes African Sub 8696 G=0.8853 A=0.1147
gnomAD - Genomes East Asian Sub 1552 G=0.9929 A=0.0071
gnomAD - Genomes Other Sub 1088 G=0.7059 A=0.2941
gnomAD - Genomes American Sub 848 G=0.787 A=0.213
gnomAD - Genomes Ashkenazi Jewish Sub 290 G=0.655 A=0.345
1000Genomes Global Study-wide 5008 G=0.8444 A=0.1556
1000Genomes African Sub 1322 G=0.9221 A=0.0779
1000Genomes East Asian Sub 1008 G=0.9921 A=0.0079
1000Genomes Europe Sub 1006 G=0.6372 A=0.3628
1000Genomes South Asian Sub 978 G=0.845 A=0.155
1000Genomes American Sub 694 G=0.782 A=0.218
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.6645 A=0.3355
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.6728 A=0.3272
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.6715 A=0.3285
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9997 A=0.0003
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 G=0.8162 A=0.1838
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 G=0.985 A=0.015
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 G=0.821 A=0.179
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 G=0.554 A=0.446
HGDP-CEPH-db Supplement 1 Europe Sub 320 G=0.622 A=0.378
HGDP-CEPH-db Supplement 1 Africa Sub 242 G=0.909 A=0.091
HGDP-CEPH-db Supplement 1 America Sub 216 G=0.986 A=0.014
HGDP-CEPH-db Supplement 1 Oceania Sub 72 G=1.00 A=0.00
HapMap Global Study-wide 1726 G=0.8424 A=0.1576
HapMap American Sub 770 G=0.836 A=0.164
HapMap African Sub 690 G=0.914 A=0.086
HapMap Europe Sub 176 G=0.506 A=0.494
HapMap Asian Sub 90 G=1.00 A=0.00
Genome-wide autozygosity in Daghestan Global Study-wide 1134 G=0.7072 A=0.2928
Genome-wide autozygosity in Daghestan Daghestan Sub 628 G=0.685 A=0.315
Genome-wide autozygosity in Daghestan Near_East Sub 144 G=0.667 A=0.333
Genome-wide autozygosity in Daghestan Central Asia Sub 122 G=0.779 A=0.221
Genome-wide autozygosity in Daghestan Europe Sub 106 G=0.623 A=0.377
Genome-wide autozygosity in Daghestan South Asian Sub 98 G=0.93 A=0.07
Genome-wide autozygosity in Daghestan Caucasus Sub 36 G=0.67 A=0.33
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.627 A=0.373
Chileans Chilean Study-wide 626 G=0.792 A=0.208
Northern Sweden ACPOP Study-wide 600 G=0.667 A=0.333
Qatari Global Study-wide 216 G=0.685 A=0.315
A Vietnamese Genetic Variation Database Global Study-wide 214 G=0.981 A=0.019
SGDP_PRJ Global Study-wide 140 G=0.443 A=0.557
The Danish reference pan genome Danish Study-wide 40 G=0.78 A=0.23
Siberian Global Study-wide 8 G=0.2 A=0.8
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 G= A
GRCh38.p12 chr 16 NC_000016.10:g.81225291= NC_000016.10:g.81225291G>A
GRCh37.p13 chr 16 NC_000016.9:g.81258896= NC_000016.9:g.81258896G>A
PKD1L2 RefSeqGene NG_033236.1:g.80= NG_033236.1:g.80C>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#.

81 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 CSHL-HAPMAP ss16715604 Feb 28, 2004 (120)
2 AFFY ss66069228 Nov 29, 2006 (127)
3 ILLUMINA ss66733255 Nov 29, 2006 (127)
4 ILLUMINA ss66940161 Nov 29, 2006 (127)
5 ILLUMINA ss67101309 Nov 29, 2006 (127)
6 PERLEGEN ss69351261 May 16, 2007 (127)
7 ILLUMINA ss70396285 May 16, 2007 (127)
8 ILLUMINA ss70534170 May 25, 2008 (130)
9 ILLUMINA ss71065299 May 16, 2007 (127)
10 ILLUMINA ss75685700 Dec 07, 2007 (129)
11 AFFY ss75996918 Dec 07, 2007 (129)
12 HGSV ss78317196 Dec 07, 2007 (129)
13 KRIBB_YJKIM ss85112363 Dec 15, 2007 (130)
14 BCMHGSC_JDW ss90466936 Mar 24, 2008 (129)
15 ILLUMINA ss121485553 Dec 01, 2009 (131)
16 ILLUMINA ss153017489 Dec 01, 2009 (131)
17 ILLUMINA ss159180913 Dec 01, 2009 (131)
18 ENSEMBL ss161809190 Dec 01, 2009 (131)
19 COMPLETE_GENOMICS ss168559040 Jul 04, 2010 (132)
20 ILLUMINA ss169901922 Jul 04, 2010 (132)
21 AFFY ss170180852 Jul 04, 2010 (132)
22 ILLUMINA ss171382672 Jul 04, 2010 (132)
23 COMPLETE_GENOMICS ss171583856 Jul 04, 2010 (132)
24 BCM-HGSC-SUB ss207568312 Jul 04, 2010 (132)
25 1000GENOMES ss210901712 Jul 14, 2010 (132)
26 1000GENOMES ss227362361 Jul 14, 2010 (132)
27 1000GENOMES ss237111133 Jul 15, 2010 (132)
28 BL ss255840341 May 09, 2011 (134)
29 PAGE_STUDY ss469414416 May 04, 2012 (137)
30 ILLUMINA ss479303089 May 04, 2012 (137)
31 ILLUMINA ss483563848 May 04, 2012 (137)
32 ILLUMINA ss532876272 Sep 08, 2015 (146)
33 TISHKOFF ss565045840 Apr 25, 2013 (138)
34 SSMP ss660825251 Apr 25, 2013 (138)
35 ILLUMINA ss779561504 Sep 08, 2015 (146)
36 ILLUMINA ss780947853 Sep 08, 2015 (146)
37 ILLUMINA ss825365680 Apr 01, 2015 (144)
38 ILLUMINA ss832693423 Jul 13, 2019 (153)
39 ILLUMINA ss835032646 Sep 08, 2015 (146)
40 EVA-GONL ss992729980 Aug 21, 2014 (142)
41 JMKIDD_LAB ss1080796686 Aug 21, 2014 (142)
42 1000GENOMES ss1357170731 Aug 21, 2014 (142)
43 HAMMER_LAB ss1397722017 Sep 08, 2015 (146)
44 EVA_GENOME_DK ss1578009770 Apr 01, 2015 (144)
45 EVA_UK10K_ALSPAC ss1634918441 Apr 01, 2015 (144)
46 EVA_UK10K_TWINSUK ss1677912474 Apr 01, 2015 (144)
47 EVA_SVP ss1713556084 Apr 01, 2015 (144)
48 WEILL_CORNELL_DGM ss1936162027 Feb 12, 2016 (147)
49 JJLAB ss2028869685 Sep 14, 2016 (149)
50 USC_VALOUEV ss2157309457 Dec 20, 2016 (150)
51 HUMAN_LONGEVITY ss2214064744 Dec 20, 2016 (150)
52 TOPMED ss2378839164 Dec 20, 2016 (150)
53 ILLUMINA ss2633347580 Nov 08, 2017 (151)
54 ILLUMINA ss2635066229 Nov 08, 2017 (151)
55 GNOMAD ss2945655440 Nov 08, 2017 (151)
56 SWEGEN ss3014888965 Nov 08, 2017 (151)
57 BIOINF_KMB_FNS_UNIBA ss3028251683 Nov 08, 2017 (151)
58 TOPMED ss3252637593 Nov 08, 2017 (151)
59 CSHL ss3351556882 Nov 08, 2017 (151)
60 ILLUMINA ss3627577225 Oct 12, 2018 (152)
61 ILLUMINA ss3631332141 Oct 12, 2018 (152)
62 ILLUMINA ss3638138177 Oct 12, 2018 (152)
63 ILLUMINA ss3639080004 Oct 12, 2018 (152)
64 ILLUMINA ss3639546494 Oct 12, 2018 (152)
65 ILLUMINA ss3641969319 Oct 12, 2018 (152)
66 ILLUMINA ss3643118351 Oct 12, 2018 (152)
67 ILLUMINA ss3652141719 Oct 12, 2018 (152)
68 EGCUT_WGS ss3681870118 Jul 13, 2019 (153)
69 EVA_DECODE ss3699715050 Jul 13, 2019 (153)
70 ACPOP ss3741706867 Jul 13, 2019 (153)
71 EVA ss3754218376 Jul 13, 2019 (153)
72 PACBIO ss3788099297 Jul 13, 2019 (153)
73 PACBIO ss3793072084 Jul 13, 2019 (153)
74 PACBIO ss3797957224 Jul 13, 2019 (153)
75 KHV_HUMAN_GENOMES ss3819495465 Jul 13, 2019 (153)
76 EVA ss3834682354 Apr 27, 2020 (154)
77 EVA ss3840947119 Apr 27, 2020 (154)
78 EVA ss3846440174 Apr 27, 2020 (154)
79 HGDP ss3847552436 Apr 27, 2020 (154)
80 SGDP_PRJ ss3884923009 Apr 27, 2020 (154)
81 KRGDB ss3934469750 Apr 27, 2020 (154)
82 1000Genomes NC_000016.9 - 81258896 Oct 12, 2018 (152)
83 The Avon Longitudinal Study of Parents and Children NC_000016.9 - 81258896 Oct 12, 2018 (152)
84 Chileans NC_000016.9 - 81258896 Apr 27, 2020 (154)
85 Genome-wide autozygosity in Daghestan NC_000016.8 - 79816397 Apr 27, 2020 (154)
86 Genetic variation in the Estonian population NC_000016.9 - 81258896 Oct 12, 2018 (152)
87 The Danish reference pan genome NC_000016.9 - 81258896 Apr 27, 2020 (154)
88 gnomAD - Genomes NC_000016.9 - 81258896 Jul 13, 2019 (153)
89 Genome of the Netherlands Release 5 NC_000016.9 - 81258896 Apr 27, 2020 (154)
90 HGDP-CEPH-db Supplement 1 NC_000016.8 - 79816397 Apr 27, 2020 (154)
91 HapMap NC_000016.10 - 81225291 Apr 27, 2020 (154)
92 KOREAN population from KRGDB NC_000016.9 - 81258896 Apr 27, 2020 (154)
93 Northern Sweden NC_000016.9 - 81258896 Jul 13, 2019 (153)
94 Qatari NC_000016.9 - 81258896 Apr 27, 2020 (154)
95 SGDP_PRJ NC_000016.9 - 81258896 Apr 27, 2020 (154)
96 Siberian NC_000016.9 - 81258896 Apr 27, 2020 (154)
97 TopMed NC_000016.10 - 81225291 Oct 12, 2018 (152)
98 UK 10K study - Twins NC_000016.9 - 81258896 Oct 12, 2018 (152)
99 A Vietnamese Genetic Variation Database NC_000016.9 - 81258896 Jul 13, 2019 (153)
100 dbGaP Population Frequency Project NC_000016.10 - 81225291 Apr 27, 2020 (154)
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)
rs59186027 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
191963, 230328, ss78317196, ss90466936, ss168559040, ss171583856, ss207568312, ss210901712, ss255840341, ss483563848, ss825365680, ss1397722017, ss1713556084, ss2635066229, ss3639080004, ss3639546494, ss3643118351, ss3847552436 NC_000016.8:79816396:G:A NC_000016.10:81225290:G:A (self)
70362830, 39039617, 173694, 27608366, 4218160, 192025317, 17403007, 41647144, 14991732, 18203949, 36939989, 9825811, 39039617, 8652110, ss227362361, ss237111133, ss479303089, ss532876272, ss565045840, ss660825251, ss779561504, ss780947853, ss832693423, ss835032646, ss992729980, ss1080796686, ss1357170731, ss1578009770, ss1634918441, ss1677912474, ss1936162027, ss2028869685, ss2157309457, ss2378839164, ss2633347580, ss2945655440, ss3014888965, ss3351556882, ss3627577225, ss3631332141, ss3638138177, ss3641969319, ss3652141719, ss3681870118, ss3741706867, ss3754218376, ss3788099297, ss3793072084, ss3797957224, ss3834682354, ss3840947119, ss3884923009, ss3934469750 NC_000016.9:81258895:G:A NC_000016.10:81225290:G:A (self)
1425805, 149198296, 204219142, ss2214064744, ss3028251683, ss3252637593, ss3699715050, ss3819495465, ss3846440174 NC_000016.10:81225290:G:A NC_000016.10:81225290:G:A (self)
ss66069228, ss66733255, ss66940161, ss67101309, ss69351261, ss70396285, ss70534170, ss71065299, ss75685700, ss75996918, ss85112363, ss121485553, ss153017489, ss159180913, ss161809190, ss169901922, ss170180852, ss171382672, ss469414416 NT_010498.15:34873094:G:A NC_000016.10:81225290:G:A (self)
ss16715604 NT_024797.14:7970586:G:A NC_000016.10:81225290:G:A (self)
Help

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

6 citations for rs11645428
PMID Title Author Year Journal
19185284 Common variation in the beta-carotene 15,15'-monooxygenase 1 gene affects circulating levels of carotenoids: a genome-wide association study. Ferrucci L et al. 2009 American journal of human genetics
22113863 Single nucleotide polymorphisms upstream from the β-carotene 15,15'-monoxygenase gene influence provitamin A conversion efficiency in female volunteers. Lietz G et al. 2012 The Journal of nutrition
23404124 Genetic determinants of macular pigments in women of the Carotenoids in Age-Related Eye Disease Study. Meyers KJ et al. 2013 Investigative ophthalmology & visual science
23656756 Single nucleotide polymorphisms in CETP, SLC46A1, SLC19A1, CD36, BCMO1, APOA5, and ABCA1 are significant predictors of plasma HDL in healthy adults. Clifford AJ et al. 2013 Lipids in health and disease
23696881 Imputation of variants from the 1000 Genomes Project modestly improves known associations and can identify low-frequency variant-phenotype associations undetected by HapMap based imputation. Wood AR et al. 2013 PloS one
24346170 Genetic evidence for role of carotenoids in age-related macular degeneration in the Carotenoids in Age-Related Eye Disease Study (CAREDS). Meyers KJ et al. 2014 Investigative ophthalmology & visual science
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.post536+f5d31d6