Name: rs2400669
Published: September 21, 2022
License: Open Access

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 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr14:99464786 (GRCh38.p14) 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) (+ 18 more)
T=0.43372 (12256/28258, 14KJPN)
T=0.43473 (7286/16760, 8.3KJPN)
G=0.4557 (2918/6404, 1000G_30x)
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

ALFA Allele Frequency
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: 20230706150541

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

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
Allele Frequency Aggregator	Total	Global	31120	T=0.56931	G=0.43069
Allele Frequency Aggregator	European	Sub	21230	T=0.57193	G=0.42807
Allele Frequency Aggregator	African	Sub	4786	T=0.6674	G=0.3326
Allele Frequency Aggregator	Latin American 2	Sub	2814	T=0.4151	G=0.5849
Allele Frequency Aggregator	Other	Sub	1700	T=0.5288	G=0.4712
Allele Frequency Aggregator	Latin American 1	Sub	310	T=0.561	G=0.439
Allele Frequency Aggregator	Asian	Sub	172	T=0.471	G=0.529
Allele Frequency Aggregator	South Asian	Sub	108	T=0.546	G=0.454
14KJPN	JAPANESE	Study-wide	28258	T=0.43372	G=0.56628
8.3KJPN	JAPANESE	Study-wide	16760	T=0.43473	G=0.56527
1000Genomes_30x	Global	Study-wide	6404	T=0.5443	G=0.4557
1000Genomes_30x	African	Sub	1786	T=0.6820	G=0.3180
1000Genomes_30x	Europe	Sub	1266	T=0.5750	G=0.4250
1000Genomes_30x	South Asian	Sub	1202	T=0.5067	G=0.4933
1000Genomes_30x	East Asian	Sub	1170	T=0.4299	G=0.5701
1000Genomes_30x	American	Sub	980	T=0.437	G=0.563
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

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.p14 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 X1	XM_011537231.3:c.103+917A… XM_011537231.3:c.103+917A>C	N/A	Intron Variant
SETD3 transcript variant X3	XM_011537232.4:c.103+917A… XM_011537232.4:c.103+917A>C	N/A	Intron Variant
SETD3 transcript variant X6	XM_011537233.3:c.103+917A… XM_011537233.3:c.103+917A>C	N/A	Intron Variant
SETD3 transcript variant X7	XM_011537235.1:c.103+917A… XM_011537235.1:c.103+917A>C	N/A	Intron Variant
SETD3 transcript variant X2	XM_017021699.2:c.103+917A… XM_017021699.2:c.103+917A>C	N/A	Intron Variant
SETD3 transcript variant X5	XM_017021700.2:c.103+917A… XM_017021700.2:c.103+917A>C	N/A	Intron Variant
SETD3 transcript variant X4	XM_047431805.1:c.103+917A… XM_047431805.1:c.103+917A>C	N/A	Intron Variant

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

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.p14 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 X1	XM_011537231.3:c.103+917=	XM_011537231.3:c.103+917A>C
SETD3 transcript variant X3	XM_011537232.4:c.103+917=	XM_011537232.4:c.103+917A>C
SETD3 transcript variant X6	XM_011537233.3:c.103+917=	XM_011537233.3:c.103+917A>C
SETD3 transcript variant X7	XM_011537235.1:c.103+917=	XM_011537235.1:c.103+917A>C
SETD3 transcript variant X2	XM_017021699.2:c.103+917=	XM_017021699.2:c.103+917A>C
SETD3 transcript variant X5	XM_017021700.2:c.103+917=	XM_017021700.2:c.103+917A>C
SETD3 transcript variant X4	XM_047431805.1:c.103+917=	XM_047431805.1:c.103+917A>C

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, 20 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	SYSTEMSBIOZJU	ss2628602421	Nov 08, 2017 (151)
48	GRF	ss2701047729	Nov 08, 2017 (151)
49	GNOMAD	ss2931532414	Nov 08, 2017 (151)
50	SWEGEN	ss3012756128	Nov 08, 2017 (151)
51	BIOINF_KMB_FNS_UNIBA	ss3027941499	Nov 08, 2017 (151)
52	CSHL	ss3350968600	Nov 08, 2017 (151)
53	ILLUMINA	ss3627302323	Oct 12, 2018 (152)
54	ILLUMINA	ss3638070635	Oct 12, 2018 (152)
55	ILLUMINA	ss3643055799	Oct 12, 2018 (152)
56	URBANLAB	ss3650277128	Oct 12, 2018 (152)
57	EGCUT_WGS	ss3680025966	Jul 13, 2019 (153)
58	EVA_DECODE	ss3697359108	Jul 13, 2019 (153)
59	ACPOP	ss3740687379	Jul 13, 2019 (153)
60	EVA	ss3752752339	Jul 13, 2019 (153)
61	PACBIO	ss3787762313	Jul 13, 2019 (153)
62	PACBIO	ss3792785825	Jul 13, 2019 (153)
63	PACBIO	ss3797670397	Jul 13, 2019 (153)
64	KHV_HUMAN_GENOMES	ss3818072820	Jul 13, 2019 (153)
65	EVA	ss3834097888	Apr 27, 2020 (154)
66	EVA	ss3840640749	Apr 27, 2020 (154)
67	EVA	ss3846131328	Apr 27, 2020 (154)
68	SGDP_PRJ	ss3882224996	Apr 27, 2020 (154)
69	KRGDB	ss3931312570	Apr 27, 2020 (154)
70	KOGIC	ss3975590746	Apr 27, 2020 (154)
71	EVA	ss4017688805	Apr 26, 2021 (155)
72	TOPMED	ss4982308782	Apr 26, 2021 (155)
73	TOMMO_GENOMICS	ss5214770066	Apr 26, 2021 (155)
74	1000G_HIGH_COVERAGE	ss5297418904	Oct 16, 2022 (156)
75	HUGCELL_USP	ss5491352618	Oct 16, 2022 (156)
76	EVA	ss5511360304	Oct 16, 2022 (156)
77	1000G_HIGH_COVERAGE	ss5598300454	Oct 16, 2022 (156)
78	SANFORD_IMAGENETICS	ss5656902238	Oct 16, 2022 (156)
79	TOMMO_GENOMICS	ss5768013515	Oct 16, 2022 (156)
80	YY_MCH	ss5815050512	Oct 16, 2022 (156)
81	EVA	ss5841584931	Oct 16, 2022 (156)
82	EVA	ss5851184771	Oct 16, 2022 (156)
83	EVA	ss5902725126	Oct 16, 2022 (156)
84	EVA	ss5948371213	Oct 16, 2022 (156)
85	1000Genomes	NC_000014.8 - 99931123	Oct 12, 2018 (152)
86	1000Genomes_30x	NC_000014.9 - 99464786	Oct 16, 2022 (156)
87	The Avon Longitudinal Study of Parents and Children	NC_000014.8 - 99931123	Oct 12, 2018 (152)
88	Genetic variation in the Estonian population	NC_000014.8 - 99931123	Oct 12, 2018 (152)
89	The Danish reference pan genome	NC_000014.8 - 99931123	Apr 27, 2020 (154)
90	gnomAD - Genomes	NC_000014.9 - 99464786	Apr 26, 2021 (155)
91	Genome of the Netherlands Release 5	NC_000014.8 - 99931123	Apr 27, 2020 (154)
92	HapMap	NC_000014.9 - 99464786	Apr 27, 2020 (154)
93	KOREAN population from KRGDB	NC_000014.8 - 99931123	Apr 27, 2020 (154)
94	Korean Genome Project	NC_000014.9 - 99464786	Apr 27, 2020 (154)
95	Northern Sweden	NC_000014.8 - 99931123	Jul 13, 2019 (153)
96	Qatari	NC_000014.8 - 99931123	Apr 27, 2020 (154)
97	SGDP_PRJ	NC_000014.8 - 99931123	Apr 27, 2020 (154)
98	Siberian	NC_000014.8 - 99931123	Apr 27, 2020 (154)
99	8.3KJPN	NC_000014.8 - 99931123	Apr 26, 2021 (155)
100	14KJPN	NC_000014.9 - 99464786	Oct 16, 2022 (156)
101	TopMed	NC_000014.9 - 99464786	Apr 26, 2021 (155)
102	UK 10K study - Twins	NC_000014.8 - 99931123	Oct 12, 2018 (152)
103	A Vietnamese Genetic Variation Database	NC_000014.8 - 99931123	Jul 13, 2019 (153)
104	ALFA	NC_000014.9 - 99464786	Apr 26, 2021 (155)

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, ss2628602421, ss2701047729, ss2931532414, ss3012756128, ss3350968600, ss3627302323, ss3638070635, ss3680025966, ss3740687379, ss3752752339, ss3787762313, ss3792785825, ss3797670397, ss3834097888, ss3840640749, ss3882224996, ss3931312570, ss4017688805, ss5214770066, ss5511360304, ss5656902238, ss5841584931, ss5948371213	NC_000014.8:99931122:T:G	NC_000014.9:99464785:T:G	(self)
85826389, 460961278, 1215943, 31968747, 101850619, 197854441, 12903102384, ss2204808758, ss3027941499, ss3650277128, ss3697359108, ss3818072820, ss3846131328, ss3975590746, ss4982308782, ss5297418904, ss5491352618, ss5598300454, ss5768013515, ss5815050512, ss5851184771, ss5902725126	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)

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

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs2400669