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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.

rs3781907

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr11:74005424 (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=0.29434 (36960/125568, TOPMED)
G=0.3052 (9413/30844, GnomAD)
G=0.286 (1430/5008, 1000G) (+ 3 more)
G=0.313 (1401/4480, Estonian)
G=0.275 (1061/3854, ALSPAC)
G=0.285 (1056/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
UCP3 : Intron Variant
Publications
5 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 11 NC_000011.10:g.74005424A>G
GRCh37.p13 chr 11 NC_000011.9:g.73716469A>G
UCP3 RefSeqGene NG_011515.1:g.8814T>C
Gene: UCP3, uncoupling protein 3 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
UCP3 transcript variant long NM_003356.3:c. N/A Intron Variant
UCP3 transcript variant short NM_022803.2:c. N/A Intron 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").

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Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 125568 A=0.70566 G=0.29434
gnomAD - Genomes Global Study-wide 30844 A=0.6948 G=0.3052
gnomAD - Genomes European Sub 18422 A=0.7031 G=0.2969
gnomAD - Genomes African Sub 8692 A=0.689 G=0.311
gnomAD - Genomes East Asian Sub 1614 A=0.589 G=0.411
gnomAD - Genomes Other Sub 980 A=0.71 G=0.29
gnomAD - Genomes American Sub 836 A=0.77 G=0.23
gnomAD - Genomes Ashkenazi Jewish Sub 300 A=0.68 G=0.32
1000Genomes Global Study-wide 5008 A=0.714 G=0.286
1000Genomes African Sub 1322 A=0.707 G=0.293
1000Genomes East Asian Sub 1008 A=0.613 G=0.387
1000Genomes Europe Sub 1006 A=0.732 G=0.268
1000Genomes South Asian Sub 978 A=0.75 G=0.25
1000Genomes American Sub 694 A=0.81 G=0.19
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.687 G=0.313
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.725 G=0.275
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.715 G=0.285
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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 11 NC_000011.10:g.74005424A= NC_000011.10:g.74005424A>G
GRCh37.p13 chr 11 NC_000011.9:g.73716469A= NC_000011.9:g.73716469A>G
UCP3 RefSeqGene NG_011515.1:g.8814T= NG_011515.1:g.8814T>C
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#.

84 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 YUSUKE ss4967975 Aug 28, 2002 (107)
2 ILLUMINA ss66779104 Dec 01, 2006 (127)
3 ILLUMINA ss67302507 Dec 01, 2006 (127)
4 ILLUMINA ss67707414 Dec 01, 2006 (127)
5 PERLEGEN ss69320509 May 18, 2007 (127)
6 ILLUMINA ss70781157 May 26, 2008 (130)
7 ILLUMINA ss71357601 May 18, 2007 (127)
8 ILLUMINA ss75767661 Dec 07, 2007 (129)
9 ILLUMINA ss79166845 Dec 15, 2007 (130)
10 HGSV ss82069582 Dec 15, 2007 (130)
11 HGSV ss82441034 Dec 15, 2007 (130)
12 KRIBB_YJKIM ss84181596 Dec 15, 2007 (130)
13 BCMHGSC_JDW ss88639427 Mar 24, 2008 (129)
14 BGI ss106752014 Feb 06, 2009 (130)
15 ILLUMINA ss122220617 Dec 01, 2009 (131)
16 ILLUMINA ss154268604 Dec 01, 2009 (131)
17 ILLUMINA ss159445379 Dec 01, 2009 (131)
18 ILLUMINA ss160641022 Dec 01, 2009 (131)
19 COMPLETE_GENOMICS ss168566075 Jul 04, 2010 (132)
20 ILLUMINA ss171651456 Jul 04, 2010 (132)
21 ILLUMINA ss173636928 Jul 04, 2010 (132)
22 COMPLETE_GENOMICS ss175184935 Jul 04, 2010 (132)
23 BUSHMAN ss202878148 Jul 04, 2010 (132)
24 BCM-HGSC-SUB ss207836430 Jul 04, 2010 (132)
25 1000GENOMES ss225313225 Jul 14, 2010 (132)
26 1000GENOMES ss235611331 Jul 15, 2010 (132)
27 1000GENOMES ss242233367 Jul 15, 2010 (132)
28 ILLUMINA ss244297003 Jul 04, 2010 (132)
29 BL ss255277217 May 09, 2011 (134)
30 GMI ss281065283 May 04, 2012 (137)
31 ILLUMINA ss480830997 May 04, 2012 (137)
32 ILLUMINA ss480847045 May 04, 2012 (137)
33 ILLUMINA ss481778804 Sep 08, 2015 (146)
34 ILLUMINA ss485210294 May 04, 2012 (137)
35 ILLUMINA ss537193538 Sep 08, 2015 (146)
36 TISHKOFF ss562650353 Apr 25, 2013 (138)
37 SSMP ss658166083 Apr 25, 2013 (138)
38 ILLUMINA ss778896177 Aug 21, 2014 (142)
39 ILLUMINA ss783051135 Sep 08, 2015 (146)
40 ILLUMINA ss784009693 Aug 21, 2014 (142)
41 ILLUMINA ss825497363 Jul 19, 2016 (147)
42 ILLUMINA ss832308987 Sep 08, 2015 (146)
43 ILLUMINA ss834357372 Aug 21, 2014 (142)
44 EVA-GONL ss988674673 Aug 21, 2014 (142)
45 JMKIDD_LAB ss1077832700 Aug 21, 2014 (142)
46 1000GENOMES ss1341881464 Aug 21, 2014 (142)
47 DDI ss1426675562 Apr 01, 2015 (144)
48 EVA_GENOME_DK ss1575793152 Apr 01, 2015 (144)
49 EVA_UK10K_ALSPAC ss1626893345 Apr 01, 2015 (144)
50 EVA_UK10K_TWINSUK ss1669887378 Apr 01, 2015 (144)
51 EVA_SVP ss1713264097 Apr 01, 2015 (144)
52 ILLUMINA ss1752031588 Sep 08, 2015 (146)
53 HAMMER_LAB ss1806876220 Sep 08, 2015 (146)
54 WEILL_CORNELL_DGM ss1932032389 Feb 12, 2016 (147)
55 GENOMED ss1967391167 Jul 19, 2016 (147)
56 JJLAB ss2026760364 Sep 14, 2016 (149)
57 USC_VALOUEV ss2155071105 Dec 20, 2016 (150)
58 HUMAN_LONGEVITY ss2183534257 Dec 20, 2016 (150)
59 TOPMED ss2347020466 Dec 20, 2016 (150)
60 SYSTEMSBIOZJU ss2627853891 Nov 08, 2017 (151)
61 ILLUMINA ss2632850716 Nov 08, 2017 (151)
62 ILLUMINA ss2635027736 Nov 08, 2017 (151)
63 GRF ss2699365944 Nov 08, 2017 (151)
64 GNOMAD ss2901400354 Nov 08, 2017 (151)
65 AFFY ss2984949896 Nov 08, 2017 (151)
66 AFFY ss2985592075 Nov 08, 2017 (151)
67 SWEGEN ss3008345309 Nov 08, 2017 (151)
68 BIOINF_KMB_FNS_UNIBA ss3027177414 Nov 08, 2017 (151)
69 TOPMED ss3149363831 Nov 08, 2017 (151)
70 CSHL ss3349667173 Nov 08, 2017 (151)
71 ILLUMINA ss3626689993 Oct 12, 2018 (152)
72 ILLUMINA ss3630866764 Oct 12, 2018 (152)
73 ILLUMINA ss3632990064 Oct 12, 2018 (152)
74 ILLUMINA ss3633689641 Oct 12, 2018 (152)
75 ILLUMINA ss3634463083 Oct 12, 2018 (152)
76 ILLUMINA ss3635381155 Oct 12, 2018 (152)
77 ILLUMINA ss3636146295 Oct 12, 2018 (152)
78 ILLUMINA ss3637132027 Oct 12, 2018 (152)
79 ILLUMINA ss3637915504 Oct 12, 2018 (152)
80 ILLUMINA ss3638971344 Oct 12, 2018 (152)
81 ILLUMINA ss3639486632 Oct 12, 2018 (152)
82 ILLUMINA ss3640170422 Oct 12, 2018 (152)
83 ILLUMINA ss3642913168 Oct 12, 2018 (152)
84 ILLUMINA ss3653721957 Oct 12, 2018 (152)
85 1000Genomes NC_000011.9 - 73716469 Oct 12, 2018 (152)
86 The Avon Longitudinal Study of Parents and Children NC_000011.9 - 73716469 Oct 12, 2018 (152)
87 Genetic variation in the Estonian population NC_000011.9 - 73716469 Oct 12, 2018 (152)
88 gnomAD - Genomes NC_000011.9 - 73716469 Oct 12, 2018 (152)
89 TopMed NC_000011.10 - 74005424 Oct 12, 2018 (152)
90 UK 10K study - Twins NC_000011.9 - 73716469 Oct 12, 2018 (152)
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)
rs60746296 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss82069582, ss82441034, ss88639427, ss160641022, ss168566075, ss175184935, ss202878148, ss207836430, ss244297003, ss255277217, ss281065283, ss480830997, ss825497363, ss1713264097, ss2635027736, ss3638971344, ss3639486632, ss3642913168 NC_000011.8:73394116:A= NC_000011.10:74005423:A= (self)
54424230, 30207970, 21402642, 35101876, 30207970, ss225313225, ss235611331, ss242233367, ss480847045, ss481778804, ss485210294, ss537193538, ss562650353, ss658166083, ss778896177, ss783051135, ss784009693, ss832308987, ss834357372, ss988674673, ss1077832700, ss1341881464, ss1426675562, ss1575793152, ss1626893345, ss1669887378, ss1752031588, ss1806876220, ss1932032389, ss1967391167, ss2026760364, ss2155071105, ss2347020466, ss2627853891, ss2632850716, ss2699365944, ss2901400354, ss2984949896, ss2985592075, ss3008345309, ss3349667173, ss3626689993, ss3630866764, ss3632990064, ss3633689641, ss3634463083, ss3635381155, ss3636146295, ss3637132027, ss3637915504, ss3640170422, ss3653721957 NC_000011.9:73716468:A= NC_000011.10:74005423:A= (self)
66556819, ss2183534257, ss3027177414, ss3149363831 NC_000011.10:74005423:A= NC_000011.10:74005423:A= (self)
ss4967975, ss66779104, ss67302507, ss67707414, ss69320509, ss70781157, ss71357601, ss75767661, ss79166845, ss84181596, ss106752014, ss122220617, ss154268604, ss159445379, ss171651456, ss173636928 NT_167190.1:19022263:A= NC_000011.10:74005423:A= (self)
ss82069582, ss82441034, ss88639427, ss160641022, ss168566075, ss175184935, ss202878148, ss207836430, ss244297003, ss255277217, ss281065283, ss480830997, ss825497363, ss1713264097, ss2635027736, ss3638971344, ss3639486632, ss3642913168 NC_000011.8:73394116:A>G NC_000011.10:74005423:A>G (self)
54424230, 30207970, 21402642, 35101876, 30207970, ss225313225, ss235611331, ss242233367, ss480847045, ss481778804, ss485210294, ss537193538, ss562650353, ss658166083, ss778896177, ss783051135, ss784009693, ss832308987, ss834357372, ss988674673, ss1077832700, ss1341881464, ss1426675562, ss1575793152, ss1626893345, ss1669887378, ss1752031588, ss1806876220, ss1932032389, ss1967391167, ss2026760364, ss2155071105, ss2347020466, ss2627853891, ss2632850716, ss2699365944, ss2901400354, ss2984949896, ss2985592075, ss3008345309, ss3349667173, ss3626689993, ss3630866764, ss3632990064, ss3633689641, ss3634463083, ss3635381155, ss3636146295, ss3637132027, ss3637915504, ss3640170422, ss3653721957 NC_000011.9:73716468:A>G NC_000011.10:74005423:A>G (self)
66556819, ss2183534257, ss3027177414, ss3149363831 NC_000011.10:74005423:A>G NC_000011.10:74005423:A>G (self)
ss4967975, ss66779104, ss67302507, ss67707414, ss69320509, ss70781157, ss71357601, ss75767661, ss79166845, ss84181596, ss106752014, ss122220617, ss154268604, ss159445379, ss171651456, ss173636928 NT_167190.1:19022263:A>G NC_000011.10:74005423: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.

5 citations for rs3781907
PMID Title Author Year Journal
19769793 Variation in the UCP2 and UCP3 genes associates with abdominal obesity and serum lipids: the Finnish Diabetes Prevention Study. Salopuro T et al. 2009 BMC medical genetics
20802238 Population genetic analysis of the uncoupling proteins supports a role for UCP3 in human cold resistance. Hancock AM et al. 2011 Molecular biology and evolution
21074158 Mitochondrial uncoupling protein gene cluster variation (UCP2-UCP3) and the risk of incident type 2 diabetes mellitus: the Women's Genome Health Study. Zee RY et al. 2011 Atherosclerosis
29529994 UCP2 and UCP3 variants and gene-environment interaction associated with prediabetes and T2DM in a rural population: a case control study in China. Su M et al. 2018 BMC medical genetics
29800730 The ADRA2A rs553668 variant is associated with type 2 diabetes and five variants were associated at nominal significance levels in a population-based case-control study from Mexico City. Totomoch-Serra A et al. 2018 Gene

Genomic regions, transcripts, and products
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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.post63+3f7b20b