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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.

rs1011731

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr1:172377408 (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=0.47679 (59869/125568, TOPMED)
A=0.4688 (14326/30558, GnomAD)
G=0.482 (2413/5008, 1000G) (+ 3 more)
G=0.436 (1955/4480, Estonian)
G=0.418 (1612/3854, ALSPAC)
G=0.431 (1599/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
DNM3 : Intron Variant
Publications
11 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.172377408G>A
GRCh37.p13 chr 1 NC_000001.10:g.172346548G>A
Gene: DNM3, dynamin 3 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
DNM3 transcript variant 2 NM_001136127.2:c. N/A Intron Variant
DNM3 transcript variant 4 NM_001350204.1:c. N/A Intron Variant
DNM3 transcript variant 6 NM_001350206.1:c. N/A Intron Variant
DNM3 transcript variant 1 NM_015569.4:c. N/A Intron Variant
DNM3 transcript variant 3 NM_001278252.1:c. N/A Genic Downstream Transcript Variant
DNM3 transcript variant 5 NM_001350205.1:c. N/A Genic Downstream Transcript Variant
DNM3 transcript variant 7 NR_146559.1:n. N/A Intron Variant
DNM3 transcript variant X6 XM_005245079.1:c. N/A Intron Variant
DNM3 transcript variant X1 XM_017000976.1:c. N/A Intron Variant
DNM3 transcript variant X2 XM_017000977.1:c. N/A Intron Variant
DNM3 transcript variant X3 XM_017000978.1:c. N/A Intron Variant
DNM3 transcript variant X4 XM_017000979.1:c. N/A Intron Variant
DNM3 transcript variant X5 XM_017000980.1:c. N/A Intron Variant
DNM3 transcript variant X7 XM_017000982.2:c. N/A Intron Variant
DNM3 transcript variant X8 XM_017000983.1:c. N/A Intron Variant
DNM3 transcript variant X9 XM_017000984.1:c. N/A Intron Variant
DNM3 transcript variant X10 XM_017000985.1:c. N/A Intron Variant
DNM3 transcript variant X11 XM_017000986.1:c. N/A Intron Variant
DNM3 transcript variant X12 XM_017000987.1:c. N/A Intron Variant
DNM3 transcript variant X13 XM_017000988.1:c. N/A Genic Downstream Transcript Variant
DNM3 transcript variant X15 XM_017000989.1:c. N/A Genic Downstream Transcript Variant
DNM3 transcript variant X17 XM_017000990.2:c. N/A Genic Downstream Transcript Variant
DNM3 transcript variant X18 XM_017000991.1:c. N/A Genic Downstream Transcript Variant
DNM3 transcript variant X21 XM_017000992.1:c. N/A Genic Downstream Transcript Variant
DNM3 transcript variant X14 XR_001737107.1:n. N/A Intron Variant
DNM3 transcript variant X16 XR_001737108.1:n. N/A Intron Variant
DNM3 transcript variant X19 XR_001737110.1:n. N/A Intron Variant
DNM3 transcript variant X20 XR_001737111.1:n. 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
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").

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Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 125568 G=0.52321 A=0.47679
gnomAD - Genomes Global Study-wide 30558 G=0.5312 A=0.4688
gnomAD - Genomes European Sub 18290 G=0.4340 A=0.5660
gnomAD - Genomes African Sub 8626 G=0.846 A=0.154
gnomAD - Genomes East Asian Sub 1566 G=0.117 A=0.883
gnomAD - Genomes Other Sub 964 G=0.45 A=0.55
gnomAD - Genomes American Sub 810 G=0.30 A=0.70
gnomAD - Genomes Ashkenazi Jewish Sub 302 G=0.46 A=0.54
1000Genomes Global Study-wide 5008 G=0.482 A=0.518
1000Genomes African Sub 1322 G=0.902 A=0.098
1000Genomes East Asian Sub 1008 G=0.130 A=0.870
1000Genomes Europe Sub 1006 G=0.417 A=0.583
1000Genomes South Asian Sub 978 G=0.43 A=0.57
1000Genomes American Sub 694 G=0.36 A=0.64
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.436 A=0.564
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.418 A=0.582
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.431 A=0.569
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 Note
GRCh38.p12 chr 1 NC_000001.11:g.172377408G= NC_000001.11:g.17237740...

NC_000001.11:g.172377408G>A

GRCh37.p13 chr 1 NC_000001.10:g.172346548G= NC_000001.10:g.17234654...

NC_000001.10:g.172346548G>A

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#.

110 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss1474662 Oct 05, 2000 (86)
2 SC_SNP ss12999427 Dec 05, 2003 (119)
3 CSHL-HAPMAP ss16417306 Feb 27, 2004 (120)
4 CSHL-HAPMAP ss19120404 Feb 27, 2004 (120)
5 SSAHASNP ss20556986 Apr 05, 2004 (121)
6 AFFY ss66296943 Dec 01, 2006 (127)
7 ILLUMINA ss66696978 Dec 01, 2006 (127)
8 ILLUMINA ss66870762 Dec 01, 2006 (127)
9 ILLUMINA ss66948074 Dec 01, 2006 (127)
10 ILLUMINA ss70359403 May 17, 2007 (127)
11 ILLUMINA ss70466241 May 25, 2008 (130)
12 ILLUMINA ss70987503 May 17, 2007 (127)
13 ILLUMINA ss75638261 Dec 06, 2007 (129)
14 AFFY ss75965829 Dec 08, 2007 (130)
15 KRIBB_YJKIM ss83656689 Dec 15, 2007 (130)
16 HUMANGENOME_JCVI ss97983751 Feb 05, 2009 (130)
17 BGI ss106611225 Feb 05, 2009 (130)
18 1000GENOMES ss108703198 Jan 23, 2009 (130)
19 ILLUMINA ss121268288 Dec 01, 2009 (131)
20 ENSEMBL ss139167700 Dec 01, 2009 (131)
21 ILLUMINA ss152575248 Dec 01, 2009 (131)
22 GMI ss155926554 Dec 01, 2009 (131)
23 ILLUMINA ss159110255 Dec 01, 2009 (131)
24 ILLUMINA ss159865761 Dec 01, 2009 (131)
25 ILLUMINA ss169270368 Jul 04, 2010 (132)
26 ILLUMINA ss169697992 Jul 04, 2010 (132)
27 AFFY ss169773926 Jul 04, 2010 (132)
28 BCM-HGSC-SUB ss205243423 Jul 04, 2010 (132)
29 ILLUMINA ss209083016 Jul 04, 2010 (132)
30 1000GENOMES ss218718977 Jul 14, 2010 (132)
31 1000GENOMES ss230782704 Jul 14, 2010 (132)
32 1000GENOMES ss238419755 Jul 15, 2010 (132)
33 BL ss253605168 May 09, 2011 (134)
34 GMI ss276102245 May 04, 2012 (137)
35 GMI ss284175817 Apr 25, 2013 (138)
36 PJP ss290664126 May 09, 2011 (134)
37 ILLUMINA ss410769941 Sep 17, 2011 (135)
38 ILLUMINA ss479193018 May 04, 2012 (137)
39 ILLUMINA ss479195424 May 04, 2012 (137)
40 ILLUMINA ss479529354 Sep 08, 2015 (146)
41 ILLUMINA ss484397547 May 04, 2012 (137)
42 EXOME_CHIP ss491306049 May 04, 2012 (137)
43 ILLUMINA ss536578350 Sep 08, 2015 (146)
44 SSMP ss648500880 Apr 25, 2013 (138)
45 ILLUMINA ss778723532 Aug 21, 2014 (142)
46 ILLUMINA ss780680308 Aug 21, 2014 (142)
47 ILLUMINA ss782645129 Aug 21, 2014 (142)
48 ILLUMINA ss783353582 Aug 21, 2014 (142)
49 ILLUMINA ss783614479 Aug 21, 2014 (142)
50 ILLUMINA ss825329134 Jul 19, 2016 (147)
51 ILLUMINA ss831895394 Apr 01, 2015 (144)
52 ILLUMINA ss832623021 Aug 21, 2014 (142)
53 ILLUMINA ss833213710 Aug 21, 2014 (142)
54 ILLUMINA ss834182948 Aug 21, 2014 (142)
55 EVA-GONL ss975815432 Aug 21, 2014 (142)
56 JMKIDD_LAB ss1068366900 Aug 21, 2014 (142)
57 1000GENOMES ss1293426033 Aug 21, 2014 (142)
58 DDI ss1426019319 Apr 01, 2015 (144)
59 EVA_GENOME_DK ss1574477982 Apr 01, 2015 (144)
60 EVA_DECODE ss1585202178 Apr 01, 2015 (144)
61 EVA_UK10K_ALSPAC ss1601481623 Apr 01, 2015 (144)
62 EVA_UK10K_TWINSUK ss1644475656 Apr 01, 2015 (144)
63 EVA_SVP ss1712381838 Apr 01, 2015 (144)
64 ILLUMINA ss1751881694 Sep 08, 2015 (146)
65 ILLUMINA ss1751881695 Sep 08, 2015 (146)
66 HAMMER_LAB ss1795275111 Sep 08, 2015 (146)
67 ILLUMINA ss1917738457 Feb 12, 2016 (147)
68 WEILL_CORNELL_DGM ss1919053145 Feb 12, 2016 (147)
69 ILLUMINA ss1946015055 Feb 12, 2016 (147)
70 ILLUMINA ss1958332553 Feb 12, 2016 (147)
71 GENOMED ss1966899277 Jul 19, 2016 (147)
72 JJLAB ss2020042523 Sep 14, 2016 (149)
73 USC_VALOUEV ss2148069922 Dec 20, 2016 (150)
74 HUMAN_LONGEVITY ss2167548923 Dec 20, 2016 (150)
75 TOPMED ss2330092859 Dec 20, 2016 (150)
76 ILLUMINA ss2632593457 Nov 08, 2017 (151)
77 ILLUMINA ss2632593458 Nov 08, 2017 (151)
78 ILLUMINA ss2632593459 Nov 08, 2017 (151)
79 ILLUMINA ss2635004504 Nov 08, 2017 (151)
80 GRF ss2698048670 Nov 08, 2017 (151)
81 GNOMAD ss2762722933 Nov 08, 2017 (151)
82 AFFY ss2984885408 Nov 08, 2017 (151)
83 AFFY ss2985531142 Nov 08, 2017 (151)
84 SWEGEN ss2987955358 Nov 08, 2017 (151)
85 ILLUMINA ss3021151975 Nov 08, 2017 (151)
86 BIOINF_KMB_FNS_UNIBA ss3023780314 Nov 08, 2017 (151)
87 TOPMED ss3095361585 Nov 08, 2017 (151)
88 CSHL ss3343771342 Nov 08, 2017 (151)
89 ILLUMINA ss3626240934 Oct 11, 2018 (152)
90 ILLUMINA ss3626240935 Oct 11, 2018 (152)
91 ILLUMINA ss3630625103 Oct 11, 2018 (152)
92 ILLUMINA ss3632915399 Oct 11, 2018 (152)
93 ILLUMINA ss3633610981 Oct 11, 2018 (152)
94 ILLUMINA ss3634358628 Oct 11, 2018 (152)
95 ILLUMINA ss3634358629 Oct 11, 2018 (152)
96 ILLUMINA ss3635304320 Oct 11, 2018 (152)
97 ILLUMINA ss3636037526 Oct 11, 2018 (152)
98 ILLUMINA ss3637054828 Oct 11, 2018 (152)
99 ILLUMINA ss3637796265 Oct 11, 2018 (152)
100 ILLUMINA ss3638914439 Oct 11, 2018 (152)
101 ILLUMINA ss3639455609 Oct 11, 2018 (152)
102 ILLUMINA ss3640065982 Oct 11, 2018 (152)
103 ILLUMINA ss3640065983 Oct 11, 2018 (152)
104 ILLUMINA ss3640988669 Oct 11, 2018 (152)
105 ILLUMINA ss3641282725 Oct 11, 2018 (152)
106 ILLUMINA ss3642804445 Oct 11, 2018 (152)
107 ILLUMINA ss3644511011 Oct 11, 2018 (152)
108 URBANLAB ss3646819993 Oct 11, 2018 (152)
109 ILLUMINA ss3651488849 Oct 11, 2018 (152)
110 ILLUMINA ss3653654769 Oct 11, 2018 (152)
111 1000Genomes NC_000001.10 - 172346548 Oct 11, 2018 (152)
112 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 172346548 Oct 11, 2018 (152)
113 Genetic variation in the Estonian population NC_000001.10 - 172346548 Oct 11, 2018 (152)
114 gnomAD - Genomes NC_000001.10 - 172346548 Oct 11, 2018 (152)
115 TopMed NC_000001.11 - 172377408 Oct 11, 2018 (152)
116 UK 10K study - Twins NC_000001.10 - 172346548 Oct 11, 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)
rs56574651 May 25, 2008 (130)
rs59121365 May 25, 2008 (130)
rs386509987 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss3638914439, ss3639455609 NC_000001.8:169078204:G:A NC_000001.11:172377407:G:A
ss66296943, ss75965829, ss108703198, ss169773926, ss205243423, ss253605168, ss276102245, ss284175817, ss290664126, ss479193018, ss825329134, ss1585202178, ss1712381838, ss2635004504, ss3642804445 NC_000001.9:170613170:G:A NC_000001.11:172377407:G:A (self)
4235364, 2314681, 1637927, 12122132, 2314681, ss218718977, ss230782704, ss238419755, ss479195424, ss479529354, ss484397547, ss491306049, ss536578350, ss648500880, ss778723532, ss780680308, ss782645129, ss783353582, ss783614479, ss831895394, ss832623021, ss833213710, ss834182948, ss975815432, ss1068366900, ss1293426033, ss1426019319, ss1574477982, ss1601481623, ss1644475656, ss1751881694, ss1751881695, ss1795275111, ss1917738457, ss1919053145, ss1946015055, ss1958332553, ss1966899277, ss2020042523, ss2148069922, ss2330092859, ss2632593457, ss2632593458, ss2632593459, ss2698048670, ss2762722933, ss2984885408, ss2985531142, ss2987955358, ss3021151975, ss3343771342, ss3626240934, ss3626240935, ss3630625103, ss3632915399, ss3633610981, ss3634358628, ss3634358629, ss3635304320, ss3636037526, ss3637054828, ss3637796265, ss3640065982, ss3640065983, ss3640988669, ss3641282725, ss3644511011, ss3651488849, ss3653654769 NC_000001.10:172346547:G:A NC_000001.11:172377407:G:A (self)
22768821, ss2167548923, ss3023780314, ss3095361585, ss3646819993 NC_000001.11:172377407:G:A NC_000001.11:172377407:G:A (self)
ss12999427 NT_004487.15:1200105:G:A NC_000001.11:172377407:G:A (self)
ss16417306, ss19120404, ss20556986 NT_004487.16:1395039:G:A NC_000001.11:172377407:G:A (self)
ss1474662, ss66696978, ss66870762, ss66948074, ss70359403, ss70466241, ss70987503, ss75638261, ss83656689, ss97983751, ss106611225, ss121268288, ss139167700, ss152575248, ss155926554, ss159110255, ss159865761, ss169270368, ss169697992, ss209083016, ss410769941 NT_004487.19:23835189:G:A NC_000001.11:172377407: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.

11 citations for rs1011731
PMID Title Author Year Journal
20935629 Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution. Heid IM et al. 2010 Nature genetics
21466928 Genetics and epigenetics of obesity. Herrera BM et al. 2011 Maturitas
22651247 Sex differences in human adipose tissues - the biology of pear shape. Karastergiou K et al. 2012 Biology of sex differences
23221025 Replication study of 15 recently published Loci for body fat distribution in the Japanese population. Hotta K et al. 2013 Journal of atherosclerosis and thrombosis
26832135 A Genetic Risk Score Is Associated with Weight Loss Following Roux-en Y Gastric Bypass Surgery. Bandstein M et al. 2016 Obesity surgery
27023174 Exon-focused genome-wide association study of obsessive-compulsive disorder and shared polygenic risk with schizophrenia. Costas J et al. 2016 Translational psychiatry
27104953 Effects of Genetic Loci Associated with Central Obesity on Adipocyte Lipolysis. Strawbridge RJ et al. 2016 PloS one
27195708 Investigation of Genetic Variation Underlying Central Obesity amongst South Asians. Scott WR et al. 2016 PloS one
27427429 Commentary: Two-sample Mendelian randomization: opportunities and challenges. Lawlor DA et al. 2016 International journal of epidemiology
28841830 Alcohol consumption and its interaction with adiposity-associated genetic variants in relation to subsequent changes in waist circumference and body weight. Rohde JF et al. 2017 Nutrition journal
29755575 Waist-hip ratio related genetic loci are associated with risk of impaired fasting glucose in Chinese children: a case control study. Song QY et al. 2018 Nutrition & metabolism

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.post104+4a6ee9c