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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.

rs2400669

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr14:99464786 (GRCh38.p13) 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
T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.415694 (110030/264690, TOPMED)
G=0.413129 (57891/140128, GnomAD)
G=0.43069 (13403/31120, ALFA) (+ 16 more)
T=0.43473 (7286/16760, 8.3KJPN)
G=0.4529 (2268/5008, 1000G)
G=0.4779 (2141/4480, Estonian)
G=0.4113 (1585/3854, ALSPAC)
G=0.3951 (1465/3708, TWINSUK)
T=0.4197 (1229/2928, KOREAN)
T=0.4214 (772/1832, Korea1K)
G=0.4146 (733/1768, HapMap)
G=0.440 (439/998, GoNL)
G=0.478 (287/600, NorthernSweden)
T=0.332 (129/388, SGDP_PRJ)
G=0.394 (85/216, Qatari)
T=0.500 (108/216, Vietnamese)
G=0.500 (108/216, Vietnamese)
G=0.30 (12/40, GENOME_DK)
T=0.38 (15/40, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SETD3 : Intron Variant
Publications
0 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.p13 chr 14 NC_000014.9:g.99464786T>G
GRCh37.p13 chr 14 NC_000014.8:g.99931123T>G
Gene: SETD3, SET domain containing 3, actin histidine methyltransferase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SETD3 transcript variant 1 NM_032233.3:c.103+917A>C N/A Intron Variant
SETD3 transcript variant 2 NM_199123.2:c.103+917A>C N/A Intron Variant
SETD3 transcript variant X8 XM_005268127.3:c.-46+917A…

XM_005268127.3:c.-46+917A>C

N/A Intron Variant
SETD3 transcript variant X1 XM_011537231.2:c.103+917A…

XM_011537231.2:c.103+917A>C

N/A Intron Variant
SETD3 transcript variant X4 XM_011537232.3:c.103+917A…

XM_011537232.3:c.103+917A>C

N/A Intron Variant
SETD3 transcript variant X5 XM_011537233.2:c.103+917A…

XM_011537233.2:c.103+917A>C

N/A Intron Variant
SETD3 transcript variant X7 XM_011537234.1:c.-46+917A…

XM_011537234.1:c.-46+917A>C

N/A Intron Variant
SETD3 transcript variant X10 XM_011537235.1:c.103+917A…

XM_011537235.1:c.103+917A>C

N/A Intron Variant
SETD3 transcript variant X2 XM_017021699.1:c.103+917A…

XM_017021699.1:c.103+917A>C

N/A Intron Variant
SETD3 transcript variant X3 XM_017021700.1:c.103+917A…

XM_017021700.1:c.103+917A>C

N/A Intron Variant
SETD3 transcript variant X6 XM_017021701.1:c.103+917A…

XM_017021701.1:c.103+917A>C

N/A Intron Variant
SETD3 transcript variant X9 XM_017021702.1:c.-46+917A…

XM_017021702.1:c.-46+917A>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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 31120 T=0.56931 G=0.43069
European Sub 21230 T=0.57193 G=0.42807
African Sub 4786 T=0.6674 G=0.3326
African Others Sub 160 T=0.713 G=0.287
African American Sub 4626 T=0.6658 G=0.3342
Asian Sub 172 T=0.471 G=0.529
East Asian Sub 112 T=0.491 G=0.509
Other Asian Sub 60 T=0.43 G=0.57
Latin American 1 Sub 310 T=0.561 G=0.439
Latin American 2 Sub 2814 T=0.4151 G=0.5849
South Asian Sub 108 T=0.546 G=0.454
Other Sub 1700 T=0.5288 G=0.4712


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 T=0.584306 G=0.415694
gnomAD - Genomes Global Study-wide 140128 T=0.586871 G=0.413129
gnomAD - Genomes European Sub 75878 T=0.56970 G=0.43030
gnomAD - Genomes African Sub 41990 T=0.66956 G=0.33044
gnomAD - Genomes American Sub 13656 T=0.48462 G=0.51538
gnomAD - Genomes Ashkenazi Jewish Sub 3322 T=0.4952 G=0.5048
gnomAD - Genomes East Asian Sub 3132 T=0.4476 G=0.5524
gnomAD - Genomes Other Sub 2150 T=0.5716 G=0.4284
8.3KJPN JAPANESE Study-wide 16760 T=0.43473 G=0.56527
1000Genomes Global Study-wide 5008 T=0.5471 G=0.4529
1000Genomes African Sub 1322 T=0.6936 G=0.3064
1000Genomes East Asian Sub 1008 T=0.4345 G=0.5655
1000Genomes Europe Sub 1006 T=0.5706 G=0.4294
1000Genomes South Asian Sub 978 T=0.519 G=0.481
1000Genomes American Sub 694 T=0.437 G=0.563
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.5221 G=0.4779
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.5887 G=0.4113
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.6049 G=0.3951
KOREAN population from KRGDB KOREAN Study-wide 2928 T=0.4197 G=0.5803
Korean Genome Project KOREAN Study-wide 1832 T=0.4214 G=0.5786
HapMap Global Study-wide 1768 T=0.5854 G=0.4146
HapMap African Sub 680 T=0.681 G=0.319
HapMap American Sub 662 T=0.557 G=0.443
HapMap Asian Sub 250 T=0.420 G=0.580
HapMap Europe Sub 176 T=0.557 G=0.443
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.560 G=0.440
Northern Sweden ACPOP Study-wide 600 T=0.522 G=0.478
SGDP_PRJ Global Study-wide 388 T=0.332 G=0.668
Qatari Global Study-wide 216 T=0.606 G=0.394
A Vietnamese Genetic Variation Database Global Study-wide 216 T=0.500 G=0.500
The Danish reference pan genome Danish Study-wide 40 T=0.70 G=0.30
Siberian Global Study-wide 40 T=0.38 G=0.62
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 T= G
GRCh38.p13 chr 14 NC_000014.9:g.99464786= NC_000014.9:g.99464786T>G
GRCh37.p13 chr 14 NC_000014.8:g.99931123= NC_000014.8:g.99931123T>G
SETD3 transcript variant 1 NM_032233.2:c.103+917= NM_032233.2:c.103+917A>C
SETD3 transcript variant 1 NM_032233.3:c.103+917= NM_032233.3:c.103+917A>C
SETD3 transcript variant 2 NM_199123.1:c.103+917= NM_199123.1:c.103+917A>C
SETD3 transcript variant 2 NM_199123.2:c.103+917= NM_199123.2:c.103+917A>C
SETD3 transcript variant X1 XM_005268125.1:c.103+917= XM_005268125.1:c.103+917A>C
SETD3 transcript variant X2 XM_005268126.1:c.103+917= XM_005268126.1:c.103+917A>C
SETD3 transcript variant X3 XM_005268127.1:c.-46+917= XM_005268127.1:c.-46+917A>C
SETD3 transcript variant X8 XM_005268127.3:c.-46+917= XM_005268127.3:c.-46+917A>C
SETD3 transcript variant X1 XM_011537231.2:c.103+917= XM_011537231.2:c.103+917A>C
SETD3 transcript variant X4 XM_011537232.3:c.103+917= XM_011537232.3:c.103+917A>C
SETD3 transcript variant X5 XM_011537233.2:c.103+917= XM_011537233.2:c.103+917A>C
SETD3 transcript variant X7 XM_011537234.1:c.-46+917= XM_011537234.1:c.-46+917A>C
SETD3 transcript variant X10 XM_011537235.1:c.103+917= XM_011537235.1:c.103+917A>C
SETD3 transcript variant X2 XM_017021699.1:c.103+917= XM_017021699.1:c.103+917A>C
SETD3 transcript variant X3 XM_017021700.1:c.103+917= XM_017021700.1:c.103+917A>C
SETD3 transcript variant X6 XM_017021701.1:c.103+917= XM_017021701.1:c.103+917A>C
SETD3 transcript variant X9 XM_017021702.1:c.-46+917= XM_017021702.1:c.-46+917A>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#.

75 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss3364815 Sep 28, 2001 (100)
2 SC_JCM ss5724398 Feb 20, 2003 (111)
3 CSHL-HAPMAP ss16632863 Feb 27, 2004 (120)
4 CSHL-HAPMAP ss17507677 Feb 27, 2004 (120)
5 SSAHASNP ss21154331 Apr 05, 2004 (121)
6 PERLEGEN ss24210179 Sep 20, 2004 (123)
7 ILLUMINA ss65765348 Oct 16, 2006 (127)
8 AFFY ss66121860 Dec 01, 2006 (127)
9 ILLUMINA ss74855118 Dec 07, 2007 (129)
10 AFFY ss76116302 Dec 07, 2007 (129)
11 KRIBB_YJKIM ss81782192 Dec 15, 2007 (130)
12 HUMANGENOME_JCVI ss96882801 Feb 06, 2009 (130)
13 BGI ss103214519 Dec 01, 2009 (131)
14 1000GENOMES ss108611992 Jan 23, 2009 (130)
15 1000GENOMES ss113797068 Jan 25, 2009 (130)
16 ILLUMINA-UK ss118760278 Feb 14, 2009 (130)
17 ENSEMBL ss136951191 Dec 01, 2009 (131)
18 COMPLETE_GENOMICS ss168595174 Jul 04, 2010 (132)
19 COMPLETE_GENOMICS ss170557361 Jul 04, 2010 (132)
20 AFFY ss172553787 Jul 04, 2010 (132)
21 ILLUMINA ss173327418 Jul 04, 2010 (132)
22 BUSHMAN ss200494816 Jul 04, 2010 (132)
23 1000GENOMES ss226755316 Jul 14, 2010 (132)
24 1000GENOMES ss236678686 Jul 15, 2010 (132)
25 1000GENOMES ss243086177 Jul 15, 2010 (132)
26 GMI ss282135560 May 04, 2012 (137)
27 GMI ss286901964 Apr 25, 2013 (138)
28 PJP ss291664597 May 09, 2011 (134)
29 ILLUMINA ss537086795 Sep 08, 2015 (146)
30 TISHKOFF ss564310763 Apr 25, 2013 (138)
31 SSMP ss660008145 Apr 25, 2013 (138)
32 EVA-GONL ss991509315 Aug 21, 2014 (142)
33 JMKIDD_LAB ss1079929472 Aug 21, 2014 (142)
34 1000GENOMES ss1352370855 Aug 21, 2014 (142)
35 DDI ss1427530628 Apr 01, 2015 (144)
36 EVA_GENOME_DK ss1577467245 Apr 01, 2015 (144)
37 EVA_UK10K_ALSPAC ss1632475004 Apr 01, 2015 (144)
38 EVA_UK10K_TWINSUK ss1675469037 Apr 01, 2015 (144)
39 EVA_DECODE ss1695525903 Apr 01, 2015 (144)
40 EVA_SVP ss1713471619 Apr 01, 2015 (144)
41 HAMMER_LAB ss1808073637 Sep 08, 2015 (146)
42 WEILL_CORNELL_DGM ss1934879259 Feb 12, 2016 (147)
43 GENOMED ss1968044205 Jul 19, 2016 (147)
44 JJLAB ss2028225971 Sep 14, 2016 (149)
45 USC_VALOUEV ss2156610915 Dec 20, 2016 (150)
46 HUMAN_LONGEVITY ss2204808758 Dec 20, 2016 (150)
47 TOPMED ss2369213966 Dec 20, 2016 (150)
48 SYSTEMSBIOZJU ss2628602421 Nov 08, 2017 (151)
49 GRF ss2701047729 Nov 08, 2017 (151)
50 GNOMAD ss2931532414 Nov 08, 2017 (151)
51 SWEGEN ss3012756128 Nov 08, 2017 (151)
52 BIOINF_KMB_FNS_UNIBA ss3027941499 Nov 08, 2017 (151)
53 TOPMED ss3219978639 Nov 08, 2017 (151)
54 CSHL ss3350968600 Nov 08, 2017 (151)
55 ILLUMINA ss3627302323 Oct 12, 2018 (152)
56 ILLUMINA ss3638070635 Oct 12, 2018 (152)
57 ILLUMINA ss3643055799 Oct 12, 2018 (152)
58 URBANLAB ss3650277128 Oct 12, 2018 (152)
59 EGCUT_WGS ss3680025966 Jul 13, 2019 (153)
60 EVA_DECODE ss3697359108 Jul 13, 2019 (153)
61 ACPOP ss3740687379 Jul 13, 2019 (153)
62 EVA ss3752752339 Jul 13, 2019 (153)
63 PACBIO ss3787762313 Jul 13, 2019 (153)
64 PACBIO ss3792785825 Jul 13, 2019 (153)
65 PACBIO ss3797670397 Jul 13, 2019 (153)
66 KHV_HUMAN_GENOMES ss3818072820 Jul 13, 2019 (153)
67 EVA ss3834097888 Apr 27, 2020 (154)
68 EVA ss3840640749 Apr 27, 2020 (154)
69 EVA ss3846131328 Apr 27, 2020 (154)
70 SGDP_PRJ ss3882224996 Apr 27, 2020 (154)
71 KRGDB ss3931312570 Apr 27, 2020 (154)
72 KOGIC ss3975590746 Apr 27, 2020 (154)
73 EVA ss4017688805 Apr 26, 2021 (155)
74 TOPMED ss4982308782 Apr 26, 2021 (155)
75 TOMMO_GENOMICS ss5214770066 Apr 26, 2021 (155)
76 1000Genomes NC_000014.8 - 99931123 Oct 12, 2018 (152)
77 The Avon Longitudinal Study of Parents and Children NC_000014.8 - 99931123 Oct 12, 2018 (152)
78 Genetic variation in the Estonian population NC_000014.8 - 99931123 Oct 12, 2018 (152)
79 The Danish reference pan genome NC_000014.8 - 99931123 Apr 27, 2020 (154)
80 gnomAD - Genomes NC_000014.9 - 99464786 Apr 26, 2021 (155)
81 Genome of the Netherlands Release 5 NC_000014.8 - 99931123 Apr 27, 2020 (154)
82 HapMap NC_000014.9 - 99464786 Apr 27, 2020 (154)
83 KOREAN population from KRGDB NC_000014.8 - 99931123 Apr 27, 2020 (154)
84 Korean Genome Project NC_000014.9 - 99464786 Apr 27, 2020 (154)
85 Northern Sweden NC_000014.8 - 99931123 Jul 13, 2019 (153)
86 Qatari NC_000014.8 - 99931123 Apr 27, 2020 (154)
87 SGDP_PRJ NC_000014.8 - 99931123 Apr 27, 2020 (154)
88 Siberian NC_000014.8 - 99931123 Apr 27, 2020 (154)
89 8.3KJPN NC_000014.8 - 99931123 Apr 26, 2021 (155)
90 TopMed NC_000014.9 - 99464786 Apr 26, 2021 (155)
91 UK 10K study - Twins NC_000014.8 - 99931123 Oct 12, 2018 (152)
92 A Vietnamese Genetic Variation Database NC_000014.8 - 99931123 Jul 13, 2019 (153)
93 ALFA NC_000014.9 - 99464786 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)
rs17206493 Oct 08, 2004 (123)
rs58683175 Feb 27, 2009 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss66121860, ss76116302, ss108611992, ss113797068, ss118760278, ss168595174, ss170557361, ss172553787, ss200494816, ss282135560, ss286901964, ss291664597, ss1695525903, ss1713471619, ss3643055799 NC_000014.7:99000875:T:G NC_000014.9:99464785:T:G (self)
65402178, 36357735, 25764214, 3748139, 16230756, 38489964, 13972244, 16921189, 34241976, 9127269, 72739373, 36357735, 8088444, ss226755316, ss236678686, ss243086177, ss537086795, ss564310763, ss660008145, ss991509315, ss1079929472, ss1352370855, ss1427530628, ss1577467245, ss1632475004, ss1675469037, ss1808073637, ss1934879259, ss1968044205, ss2028225971, ss2156610915, ss2369213966, ss2628602421, ss2701047729, ss2931532414, ss3012756128, ss3350968600, ss3627302323, ss3638070635, ss3680025966, ss3740687379, ss3752752339, ss3787762313, ss3792785825, ss3797670397, ss3834097888, ss3840640749, ss3882224996, ss3931312570, ss4017688805, ss5214770066 NC_000014.8:99931122:T:G NC_000014.9:99464785:T:G (self)
460961278, 1215943, 31968747, 123834517, 197854441, 12903102384, ss2204808758, ss3027941499, ss3219978639, ss3650277128, ss3697359108, ss3818072820, ss3846131328, ss3975590746, ss4982308782 NC_000014.9:99464785:T:G NC_000014.9:99464785:T:G (self)
ss16632863, ss17507677, ss21154331 NT_026437.10:79851163:T:G NC_000014.9:99464785:T:G (self)
ss3364815, ss5724398, ss24210179, ss65765348, ss74855118, ss81782192, ss96882801, ss103214519, ss136951191, ss173327418 NT_026437.12:80931122:T:G NC_000014.9:99464785:T:G (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 rs2400669

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.post596+ae089ad