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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs13293564

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr9:35166766 (GRCh38.p7) 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 / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.43607 (54757/125568, TOPMED)
T=0.4479 (13838/30896, GnomAD)
T=0.359 (1797/5008, 1000G) (+ 2 more)
T=0.405 (1562/3854, ALSPAC)
T=0.397 (1471/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
UNC13B : 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.p7 chr 9 NC_000009.12:g.35166766G>A
GRCh38.p7 chr 9 NC_000009.12:g.35166766G>T
GRCh37.p13 chr 9 NC_000009.11:g.35166763G>A
GRCh37.p13 chr 9 NC_000009.11:g.35166763G>T
UNC13B RefSeqGene NG_033014.1:g.9775G>A
UNC13B RefSeqGene NG_033014.1:g.9775G>T
Gene: UNC13B, unc-13 homolog B (C. elegans) (plus strand)
Molecule type Change Amino acid[Codon] SO Term
UNC13B transcript variant 1 NM_006377.3:c. N/A Intron Variant
UNC13B transcript variant X4 XM_011517684.2:c. N/A Intron Variant
UNC13B transcript variant X5 XM_011517685.2:c. N/A Intron Variant
UNC13B transcript variant X1 XM_011517681.2:c. N/A Genic Upstream Transcript Variant
UNC13B transcript variant X2 XM_011517682.2:c. N/A Genic Upstream Transcript Variant
UNC13B transcript variant X3 XM_011517683.2:c. N/A Genic Upstream Transcript Variant
UNC13B transcript variant X5 XM_011517686.2:c. N/A Genic Upstream Transcript Variant
UNC13B transcript variant X6 XM_017014191.1:c. N/A Genic Upstream Transcript Variant
UNC13B transcript variant X7 XM_017014192.1:c. N/A Genic Upstream Transcript 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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
Trans-Omics for Precision Medicine Global Study-wide 125568 G=0.56393 T=0.43607
The Genome Aggregation Database Global Study-wide 30896 G=0.5521 T=0.4479, A=0.0000
The Genome Aggregation Database European Sub 18440 G=0.5790 T=0.4210, A=0.0000
The Genome Aggregation Database African Sub 8716 G=0.413 T=0.587, A=0.000
The Genome Aggregation Database East Asian Sub 1622 G=0.986 T=0.014, A=0.000
The Genome Aggregation Database Other Sub 978 G=0.60 T=0.40, A=0.00
The Genome Aggregation Database American Sub 838 G=0.51 T=0.49, A=0.00
The Genome Aggregation Database Ashkenazi Jewish Sub 302 G=0.56 T=0.44, A=0.00
1000Genomes Global Study-wide 5008 G=0.641 T=0.359
1000Genomes African Sub 1322 G=0.356 T=0.644
1000Genomes East Asian Sub 1008 G=0.990 T=0.010
1000Genomes Europe Sub 1006 G=0.596 T=0.404
1000Genomes South Asian Sub 978 G=0.81 T=0.19
1000Genomes American Sub 694 G=0.51 T=0.49
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.595 T=0.405
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.603 T=0.397
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 T Note
GRCh38.p7 chr 9 NC_000009.12:g.35...

NC_000009.12:g.35166766G=

NC_000009.12:g.35...

NC_000009.12:g.35166766G>A

NC_000009.12:g.35...

NC_000009.12:g.35166766G>T

GRCh37.p13 chr 9 NC_000009.11:g.35...

NC_000009.11:g.35166763G=

NC_000009.11:g.35...

NC_000009.11:g.35166763G>A

NC_000009.11:g.35...

NC_000009.11:g.35166763G>T

UNC13B RefSeqGene NG_033014.1:g.9775G= NG_033014.1:g.977...

NG_033014.1:g.9775G>A

NG_033014.1:g.977...

NG_033014.1:g.9775G>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#.

5 Frequency, 90 SubSNP submissions
No Submitter Submission ID Date (Build)
1 SSAHASNP ss22835505 Apr 05, 2004 (121)
2 PERLEGEN ss24531871 Sep 20, 2004 (123)
3 ILLUMINA ss65795720 Oct 15, 2006 (127)
4 ILLUMINA ss66670809 Nov 30, 2006 (127)
5 ILLUMINA ss67071509 Nov 30, 2006 (127)
6 ILLUMINA ss67400821 Nov 30, 2006 (127)
7 ILLUMINA ss70422281 May 17, 2007 (127)
8 ILLUMINA ss70601355 May 23, 2008 (130)
9 ILLUMINA ss71146538 May 17, 2007 (127)
10 ILLUMINA ss75582676 Dec 06, 2007 (129)
11 AFFY ss76574243 Dec 06, 2007 (129)
12 KRIBB_YJKIM ss85315253 Dec 14, 2007 (130)
13 HUMANGENOME_JCVI ss97721535 Feb 04, 2009 (130)
14 1000GENOMES ss108754253 Jan 23, 2009 (130)
15 1000GENOMES ss114450074 Jan 25, 2009 (130)
16 ILLUMINA ss121636803 Dec 01, 2009 (131)
17 ENSEMBL ss134148626 Dec 01, 2009 (131)
18 ILLUMINA ss153352042 Dec 01, 2009 (131)
19 ILLUMINA ss159252769 Dec 01, 2009 (131)
20 ILLUMINA ss160329154 Dec 01, 2009 (131)
21 COMPLETE_GENOMICS ss164087506 Jul 04, 2010 (132)
22 COMPLETE_GENOMICS ss165012952 Jul 04, 2010 (132)
23 COMPLETE_GENOMICS ss166428150 Jul 04, 2010 (132)
24 ILLUMINA ss170345119 Jul 04, 2010 (132)
25 ILLUMINA ss172381673 Jul 04, 2010 (132)
26 BUSHMAN ss200348207 Jul 04, 2010 (132)
27 BCM-HGSC-SUB ss206803011 Jul 04, 2010 (132)
28 1000GENOMES ss224230183 Jul 14, 2010 (132)
29 1000GENOMES ss234805283 Jul 15, 2010 (132)
30 BL ss254188713 May 09, 2011 (134)
31 PJP ss294438988 May 09, 2011 (134)
32 ILLUMINA ss479905194 May 04, 2012 (137)
33 ILLUMINA ss479913149 May 04, 2012 (137)
34 ILLUMINA ss480533303 Sep 08, 2015 (146)
35 ILLUMINA ss484750873 May 04, 2012 (137)
36 ILLUMINA ss536845209 Sep 08, 2015 (146)
37 TISHKOFF ss561366656 Apr 25, 2013 (138)
38 SSMP ss655810483 Apr 25, 2013 (138)
39 ILLUMINA ss778424781 Sep 08, 2015 (146)
40 ILLUMINA ss782822165 Sep 08, 2015 (146)
41 ILLUMINA ss783787210 Sep 08, 2015 (146)
42 ILLUMINA ss825391555 Apr 01, 2015 (144)
43 ILLUMINA ss832075552 Sep 08, 2015 (146)
44 ILLUMINA ss833880175 Sep 08, 2015 (146)
45 EVA-GONL ss986523643 Aug 21, 2014 (142)
46 JMKIDD_LAB ss1076279513 Aug 21, 2014 (142)
47 1000GENOMES ss1333709590 Aug 21, 2014 (142)
48 HAMMER_LAB ss1397554883 Sep 08, 2015 (146)
49 DDI ss1431816556 Apr 01, 2015 (144)
50 EVA_GENOME_DK ss1583074094 Apr 01, 2015 (144)
51 EVA_DECODE ss1596161621 Apr 01, 2015 (144)
52 EVA_UK10K_ALSPAC ss1622672337 Apr 01, 2015 (144)
53 EVA_UK10K_TWINSUK ss1665666370 Apr 01, 2015 (144)
54 EVA_SVP ss1713106597 Apr 01, 2015 (144)
55 ILLUMINA ss1752776587 Sep 08, 2015 (146)
56 HAMMER_LAB ss1805970214 Sep 08, 2015 (146)
57 WEILL_CORNELL_DGM ss1929809055 Feb 12, 2016 (147)
58 ILLUMINA ss1946257493 Feb 12, 2016 (147)
59 ILLUMINA ss1959180490 Feb 12, 2016 (147)
60 GENOMED ss1971205254 Jul 19, 2016 (147)
61 JJLAB ss2025618263 Sep 14, 2016 (149)
62 USC_VALOUEV ss2153845872 Dec 20, 2016 (150)
63 HUMAN_LONGEVITY ss2311045691 Dec 20, 2016 (150)
64 TOPMED ss2481183036 Dec 20, 2016 (150)
65 ILLUMINA ss2634862225 Nov 08, 2017 (151)
66 GRF ss2709656082 Nov 08, 2017 (151)
67 ILLUMINA ss2711162210 Nov 08, 2017 (151)
68 GNOMAD ss2877697508 Nov 08, 2017 (151)
69 SWEGEN ss3004706195 Nov 08, 2017 (151)
70 ILLUMINA ss3022925421 Nov 08, 2017 (151)
71 BIOINF_KMB_FNS_UNIBA ss3026599277 Nov 08, 2017 (151)
72 CSHL ss3348620272 Nov 08, 2017 (151)
73 TOPMED ss3587275291 Nov 08, 2017 (151)
74 ILLUMINA ss3625982960 Jul 20, 2018 (151)
75 ILLUMINA ss3630257650 Jul 20, 2018 (151)
76 ILLUMINA ss3632754849 Jul 20, 2018 (151)
77 ILLUMINA ss3633532650 Jul 20, 2018 (151)
78 ILLUMINA ss3634260871 Jul 20, 2018 (151)
79 ILLUMINA ss3635211995 Jul 20, 2018 (151)
80 ILLUMINA ss3635938918 Jul 20, 2018 (151)
81 ILLUMINA ss3636958647 Jul 20, 2018 (151)
82 ILLUMINA ss3637692211 Jul 20, 2018 (151)
83 ILLUMINA ss3638811320 Jul 20, 2018 (151)
84 ILLUMINA ss3639410613 Jul 20, 2018 (151)
85 ILLUMINA ss3639737747 Jul 20, 2018 (151)
86 ILLUMINA ss3640919285 Jul 20, 2018 (151)
87 ILLUMINA ss3641241108 Jul 20, 2018 (151)
88 ILLUMINA ss3641538991 Jul 20, 2018 (151)
89 ILLUMINA ss3643738207 Jul 20, 2018 (151)
90 ILLUMINA ss3644990814 Jul 20, 2018 (151)
91 1000Genomes NC_000009.11 - 35166763 Jul 20, 2018 (151)
92 The Avon Longitudinal Study of Parents and Children NC_000009.11 - 35166763 Jul 20, 2018 (151)
93 The Genome Aggregation Database NC_000009.11 - 35166763 Jul 20, 2018 (151)
94 Trans-Omics for Precision Medicine NC_000009.12 - 35166766 Jul 20, 2018 (151)
95 UK 10K study - Twins NC_000009.11 - 35166763 Jul 20, 2018 (151)
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)
rs17294080 Oct 08, 2004 (123)
rs57437011 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss3639410613, ss3639737747 NC_000009.9:35156762:G= NC_000009.12:35166765:G=
ss108754253, ss114450074, ss164087506, ss165012952, ss166428150, ss200348207, ss206803011, ss254188713, ss294438988, ss479905194, ss825391555, ss1397554883, ss1596161621, ss1713106597, ss3643738207 NC_000009.10:35156762:G= NC_000009.12:35166765:G= (self)
45963212, 25566336, 218325263, 25566336, ss224230183, ss234805283, ss479913149, ss480533303, ss484750873, ss536845209, ss561366656, ss655810483, ss778424781, ss782822165, ss783787210, ss832075552, ss833880175, ss986523643, ss1076279513, ss1333709590, ss1431816556, ss1583074094, ss1622672337, ss1665666370, ss1752776587, ss1805970214, ss1929809055, ss1946257493, ss1959180490, ss1971205254, ss2025618263, ss2153845872, ss2481183036, ss2634862225, ss2709656082, ss2711162210, ss2877697508, ss3004706195, ss3022925421, ss3348620272, ss3625982960, ss3630257650, ss3632754849, ss3633532650, ss3634260871, ss3635211995, ss3635938918, ss3636958647, ss3637692211, ss3638811320, ss3640919285, ss3641241108, ss3641538991, ss3644990814 NC_000009.11:35166762:G= NC_000009.12:35166765:G= (self)
410480346, ss2311045691, ss3026599277, ss3587275291 NC_000009.12:35166765:G= NC_000009.12:35166765:G= (self)
ss22835505 NT_008413.16:35156762:G= NC_000009.12:35166765:G= (self)
ss24531871, ss65795720, ss66670809, ss67071509, ss67400821, ss70422281, ss70601355, ss71146538, ss75582676, ss76574243, ss85315253, ss97721535, ss121636803, ss134148626, ss153352042, ss159252769, ss160329154, ss170345119, ss172381673 NT_008413.18:35156762:G= NC_000009.12:35166765:G= (self)
218325263, ss2877697508 NC_000009.11:35166762:G>A NC_000009.12:35166765:G>A (self)
ss3639410613, ss3639737747 NC_000009.9:35156762:G>T NC_000009.12:35166765:G>T
ss108754253, ss114450074, ss164087506, ss165012952, ss166428150, ss200348207, ss206803011, ss254188713, ss294438988, ss479905194, ss825391555, ss1397554883, ss1596161621, ss1713106597, ss3643738207 NC_000009.10:35156762:G>T NC_000009.12:35166765:G>T (self)
45963212, 25566336, 218325263, 25566336, ss224230183, ss234805283, ss479913149, ss480533303, ss484750873, ss536845209, ss561366656, ss655810483, ss778424781, ss782822165, ss783787210, ss832075552, ss833880175, ss986523643, ss1076279513, ss1333709590, ss1431816556, ss1583074094, ss1622672337, ss1665666370, ss1752776587, ss1805970214, ss1929809055, ss1946257493, ss1959180490, ss1971205254, ss2025618263, ss2153845872, ss2481183036, ss2634862225, ss2709656082, ss2711162210, ss2877697508, ss3004706195, ss3022925421, ss3348620272, ss3625982960, ss3630257650, ss3632754849, ss3633532650, ss3634260871, ss3635211995, ss3635938918, ss3636958647, ss3637692211, ss3638811320, ss3640919285, ss3641241108, ss3641538991, ss3644990814 NC_000009.11:35166762:G>T NC_000009.12:35166765:G>T (self)
410480346, ss2311045691, ss3026599277, ss3587275291 NC_000009.12:35166765:G>T NC_000009.12:35166765:G>T (self)
ss22835505 NT_008413.16:35156762:G>T NC_000009.12:35166765:G>T (self)
ss24531871, ss65795720, ss66670809, ss67071509, ss67400821, ss70422281, ss70601355, ss71146538, ss75582676, ss76574243, ss85315253, ss97721535, ss121636803, ss134148626, ss153352042, ss159252769, ss160329154, ss170345119, ss172381673 NT_008413.18:35156762:G>T NC_000009.12:35166765:G>T (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 rs13293564
PMID Title Author Year Journal
18633107 G/T substitution in intron 1 of the UNC13B gene is associated with increased risk of nephropathy in patients with type 1 diabetes. Trégouet DA et al. 2008 Diabetes
20687937 Genome-wide DNA methylation analysis for diabetic nephropathy in type 1 diabetes mellitus. Bell CG et al. 2010 BMC medical genomics
21127830 Genetic associations in diabetic nephropathy: a meta-analysis. Mooyaart AL et al. 2011 Diabetologia
26798653 A Systems Biology Overview on Human Diabetic Nephropathy: From Genetic Susceptibility to Post-Transcriptional and Post-Translational Modifications. Conserva F et al. 2016 Journal of diabetes research
27042264 Genetics of cardiovascular and renal complications in diabetes. Ma RC et al. 2016 Journal of diabetes investigation

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: 0.1.4.post833+d3ba21e