Name: rs4040604
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.

rs4040604

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:927744 (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: G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.240576 (63678/264690, TOPMED)
G=0.220753 (30954/140220, GnomAD)
G=0.45952 (12985/28258, 14KJPN) (+ 17 more)
G=0.15184 (3089/20344, ALFA)
G=0.45955 (7702/16760, 8.3KJPN)
G=0.3262 (2089/6404, 1000G_30x)
G=0.3199 (1602/5008, 1000G)
G=0.0317 (142/4480, Estonian)
G=0.0236 (91/3854, ALSPAC)
G=0.0235 (87/3708, TWINSUK)
G=0.4621 (1353/2928, KOREAN)
G=0.3779 (715/1892, HapMap)
G=0.4607 (844/1832, Korea1K)
G=0.017 (17/998, GoNL)
G=0.025 (15/600, NorthernSweden)
G=0.169 (80/474, SGDP_PRJ)
G=0.171 (37/216, Qatari)
G=0.411 (88/214, Vietnamese)
G=0.05 (3/56, Siberian)
G=0.00 (0/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: SAMD11 : 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	20344	G=0.15184	T=0.84816
European	Sub	14294	G=0.02833	T=0.97167
African	Sub	4084	G=0.5769	T=0.4231
African Others	Sub	144	G=0.694	T=0.306
African American	Sub	3940	G=0.5726	T=0.4274
Asian	Sub	116	G=0.457	T=0.543
East Asian	Sub	88	G=0.49	T=0.51
Other Asian	Sub	28	G=0.36	T=0.64
Latin American 1	Sub	154	G=0.234	T=0.766
Latin American 2	Sub	616	G=0.135	T=0.865
South Asian	Sub	98	G=0.10	T=0.90
Other	Sub	982	G=0.149	T=0.851

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	264690	G=0.240576	T=0.759424
gnomAD - Genomes	Global	Study-wide	140220	G=0.220753	T=0.779247
gnomAD - Genomes	European	Sub	75956	G=0.02944	T=0.97056
gnomAD - Genomes	African	Sub	42000	G=0.58179	T=0.41821
gnomAD - Genomes	American	Sub	13660	G=0.17189	T=0.82811
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	G=0.0427	T=0.9573
gnomAD - Genomes	East Asian	Sub	3128	G=0.4258	T=0.5742
gnomAD - Genomes	Other	Sub	2152	G=0.2142	T=0.7858
14KJPN	JAPANESE	Study-wide	28258	G=0.45952	T=0.54048
Allele Frequency Aggregator	Total	Global	20344	G=0.15184	T=0.84816
Allele Frequency Aggregator	European	Sub	14294	G=0.02833	T=0.97167
Allele Frequency Aggregator	African	Sub	4084	G=0.5769	T=0.4231
Allele Frequency Aggregator	Other	Sub	982	G=0.149	T=0.851
Allele Frequency Aggregator	Latin American 2	Sub	616	G=0.135	T=0.865
Allele Frequency Aggregator	Latin American 1	Sub	154	G=0.234	T=0.766
Allele Frequency Aggregator	Asian	Sub	116	G=0.457	T=0.543
Allele Frequency Aggregator	South Asian	Sub	98	G=0.10	T=0.90
8.3KJPN	JAPANESE	Study-wide	16760	G=0.45955	T=0.54045
1000Genomes_30x	Global	Study-wide	6404	G=0.3262	T=0.6738
1000Genomes_30x	African	Sub	1786	G=0.6753	T=0.3247
1000Genomes_30x	Europe	Sub	1266	G=0.0229	T=0.9771
1000Genomes_30x	South Asian	Sub	1202	G=0.1314	T=0.8686
1000Genomes_30x	East Asian	Sub	1170	G=0.4538	T=0.5462
1000Genomes_30x	American	Sub	980	G=0.168	T=0.832
1000Genomes	Global	Study-wide	5008	G=0.3199	T=0.6801
1000Genomes	African	Sub	1322	G=0.6657	T=0.3343
1000Genomes	East Asian	Sub	1008	G=0.4524	T=0.5476
1000Genomes	Europe	Sub	1006	G=0.0249	T=0.9751
1000Genomes	South Asian	Sub	978	G=0.125	T=0.875
1000Genomes	American	Sub	694	G=0.171	T=0.829
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.0317	T=0.9683
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.0236	T=0.9764
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.0235	T=0.9765
KOREAN population from KRGDB	KOREAN	Study-wide	2928	G=0.4621	T=0.5379
HapMap	Global	Study-wide	1892	G=0.3779	T=0.6221
HapMap	American	Sub	770	G=0.238	T=0.762
HapMap	African	Sub	692	G=0.594	T=0.406
HapMap	Asian	Sub	254	G=0.453	T=0.547
HapMap	Europe	Sub	176	G=0.034	T=0.966
Korean Genome Project	KOREAN	Study-wide	1832	G=0.4607	T=0.5393
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.017	T=0.983
Northern Sweden	ACPOP	Study-wide	600	G=0.025	T=0.975
SGDP_PRJ	Global	Study-wide	474	G=0.169	T=0.831
Qatari	Global	Study-wide	216	G=0.171	T=0.829
A Vietnamese Genetic Variation Database	Global	Study-wide	214	G=0.411	T=0.589
Siberian	Global	Study-wide	56	G=0.05	T=0.95
The Danish reference pan genome	Danish	Study-wide	40	G=0.00	T=1.00

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 1	NC_000001.11:g.927744G>T
GRCh37.p13 chr 1	NC_000001.10:g.863124G>T

Gene: SAMD11, sterile alpha motif domain containing 11 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SAMD11 transcript variant 2	NM_001385640.1:c.609+1731… NM_001385640.1:c.609+1731G>T	N/A	Intron Variant
SAMD11 transcript variant 1	NM_001385641.1:c.609+1731… NM_001385641.1:c.609+1731G>T	N/A	Intron Variant
SAMD11 transcript variant 3	NM_152486.4:c.72+1731G>T	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	G=	T
GRCh38.p14 chr 1	NC_000001.11:g.927744=	NC_000001.11:g.927744G>T
GRCh37.p13 chr 1	NC_000001.10:g.863124=	NC_000001.10:g.863124G>T
SAMD11 transcript variant 2	NM_001385640.1:c.609+1731=	NM_001385640.1:c.609+1731G>T
SAMD11 transcript variant 1	NM_001385641.1:c.609+1731=	NM_001385641.1:c.609+1731G>T
SAMD11 transcript	NM_152486.2:c.72+1731=	NM_152486.2:c.72+1731G>T
SAMD11 transcript variant 3	NM_152486.4:c.72+1731=	NM_152486.4:c.72+1731G>T
SAMD11 transcript variant X1	XM_005244723.1:c.72+1731=	XM_005244723.1:c.72+1731G>T
SAMD11 transcript variant X2	XM_005244724.1:c.72+1731=	XM_005244724.1:c.72+1731G>T
SAMD11 transcript variant X3	XM_005244725.1:c.72+1731=	XM_005244725.1:c.72+1731G>T
SAMD11 transcript variant X4	XM_005244726.1:c.72+1731=	XM_005244726.1:c.72+1731G>T
SAMD11 transcript variant X5	XM_005244727.1:c.72+1731=	XM_005244727.1:c.72+1731G>T

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#.

83 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss5397733	Oct 10, 2002 (108)
2	SC_JCM	ss5956368	Feb 20, 2003 (111)
3	SSAHASNP	ss22883050	Apr 05, 2004 (121)
4	ABI	ss41345645	Mar 15, 2006 (126)
5	ILLUMINA	ss75010777	Dec 06, 2007 (129)
6	HGSV	ss78647336	Dec 06, 2007 (129)
7	BCMHGSC_JDW	ss87156742	Mar 23, 2008 (129)
8	HUMANGENOME_JCVI	ss97913351	Feb 05, 2009 (130)
9	BGI	ss105111861	Dec 01, 2009 (131)
10	1000GENOMES	ss107938340	Jan 22, 2009 (130)
11	1000GENOMES	ss109938360	Jan 24, 2009 (130)
12	ILLUMINA-UK	ss118438913	Feb 14, 2009 (130)
13	KRIBB_YJKIM	ss119469535	Dec 01, 2009 (131)
14	ENSEMBL	ss137753523	Dec 01, 2009 (131)
15	ENSEMBL	ss138874237	Dec 01, 2009 (131)
16	COMPLETE_GENOMICS	ss162981395	Jul 04, 2010 (132)
17	COMPLETE_GENOMICS	ss163703654	Jul 04, 2010 (132)
18	COMPLETE_GENOMICS	ss165981272	Jul 04, 2010 (132)
19	ILLUMINA	ss173681055	Jul 04, 2010 (132)
20	BUSHMAN	ss197886320	Jul 04, 2010 (132)
21	BCM-HGSC-SUB	ss205234590	Jul 04, 2010 (132)
22	1000GENOMES	ss218190974	Jul 14, 2010 (132)
23	1000GENOMES	ss230395858	Jul 14, 2010 (132)
24	1000GENOMES	ss238115431	Jul 15, 2010 (132)
25	BL	ss252865278	May 09, 2011 (134)
26	GMI	ss275681737	May 04, 2012 (137)
27	GMI	ss283987785	Apr 25, 2013 (138)
28	PJP	ss290494007	May 09, 2011 (134)
29	ILLUMINA	ss537212515	Sep 08, 2015 (146)
30	TISHKOFF	ss553711183	Apr 25, 2013 (138)
31	SSMP	ss647517080	Apr 25, 2013 (138)
32	EVA-GONL	ss974770152	Aug 21, 2014 (142)
33	JMKIDD_LAB	ss1067612707	Aug 21, 2014 (142)
34	1000GENOMES	ss1289342348	Aug 21, 2014 (142)
35	DDI	ss1425685220	Apr 01, 2015 (144)
36	EVA_GENOME_DK	ss1573851401	Apr 01, 2015 (144)
37	EVA_DECODE	ss1584130058	Apr 01, 2015 (144)
38	EVA_UK10K_ALSPAC	ss1599379347	Apr 01, 2015 (144)
39	EVA_UK10K_TWINSUK	ss1642373380	Apr 01, 2015 (144)
40	EVA_SVP	ss1712305475	Apr 01, 2015 (144)
41	HAMMER_LAB	ss1793710023	Sep 08, 2015 (146)
42	WEILL_CORNELL_DGM	ss1917961590	Feb 12, 2016 (147)
43	JJLAB	ss2019498806	Sep 14, 2016 (149)
44	USC_VALOUEV	ss2147485356	Dec 20, 2016 (150)
45	HUMAN_LONGEVITY	ss2159370397	Dec 20, 2016 (150)
46	SYSTEMSBIOZJU	ss2624264967	Nov 08, 2017 (151)
47	GRF	ss2697376297	Nov 08, 2017 (151)
48	GNOMAD	ss2750648949	Nov 08, 2017 (151)
49	SWEGEN	ss2986151001	Nov 08, 2017 (151)
50	BIOINF_KMB_FNS_UNIBA	ss3023513863	Nov 08, 2017 (151)
51	CSHL	ss3343273217	Nov 08, 2017 (151)
52	ILLUMINA	ss3626006638	Oct 11, 2018 (152)
53	ILLUMINA	ss3637732385	Oct 11, 2018 (152)
54	ILLUMINA	ss3642746691	Oct 11, 2018 (152)
55	URBANLAB	ss3646581402	Oct 11, 2018 (152)
56	EGCUT_WGS	ss3654262252	Jul 12, 2019 (153)
57	EVA_DECODE	ss3685993617	Jul 12, 2019 (153)
58	ACPOP	ss3726717002	Jul 12, 2019 (153)
59	EVA	ss3745721868	Jul 12, 2019 (153)
60	PACBIO	ss3783302537	Jul 12, 2019 (153)
61	PACBIO	ss3788980200	Jul 12, 2019 (153)
62	PACBIO	ss3793852760	Jul 12, 2019 (153)
63	KHV_HUMAN_GENOMES	ss3798744555	Jul 12, 2019 (153)
64	EVA	ss3825981763	Apr 25, 2020 (154)
65	EVA	ss3836378587	Apr 25, 2020 (154)
66	EVA	ss3841782606	Apr 25, 2020 (154)
67	SGDP_PRJ	ss3847998069	Apr 25, 2020 (154)
68	KRGDB	ss3892840059	Apr 25, 2020 (154)
69	KOGIC	ss3943631572	Apr 25, 2020 (154)
70	EVA	ss4016889054	Apr 25, 2021 (155)
71	TOPMED	ss4436457050	Apr 25, 2021 (155)
72	TOMMO_GENOMICS	ss5142056735	Apr 25, 2021 (155)
73	1000G_HIGH_COVERAGE	ss5240866367	Oct 12, 2022 (156)
74	EVA	ss5316188156	Oct 12, 2022 (156)
75	HUGCELL_USP	ss5442114169	Oct 12, 2022 (156)
76	1000G_HIGH_COVERAGE	ss5512492145	Oct 12, 2022 (156)
77	SANFORD_IMAGENETICS	ss5624751401	Oct 12, 2022 (156)
78	TOMMO_GENOMICS	ss5666197545	Oct 12, 2022 (156)
79	YY_MCH	ss5800244635	Oct 12, 2022 (156)
80	EVA	ss5831419721	Oct 12, 2022 (156)
81	EVA	ss5848749115	Oct 12, 2022 (156)
82	EVA	ss5906707149	Oct 12, 2022 (156)
83	EVA	ss5936584013	Oct 12, 2022 (156)
84	1000Genomes	NC_000001.10 - 863124	Oct 11, 2018 (152)
85	1000Genomes_30x	NC_000001.11 - 927744	Oct 12, 2022 (156)
86	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 863124	Oct 11, 2018 (152)
87	Genetic variation in the Estonian population	NC_000001.10 - 863124	Oct 11, 2018 (152)
88	The Danish reference pan genome	NC_000001.10 - 863124	Apr 25, 2020 (154)
89	gnomAD - Genomes	NC_000001.11 - 927744	Apr 25, 2021 (155)
90	Genome of the Netherlands Release 5	NC_000001.10 - 863124	Apr 25, 2020 (154)
91	HapMap	NC_000001.11 - 927744	Apr 25, 2020 (154)
92	KOREAN population from KRGDB	NC_000001.10 - 863124	Apr 25, 2020 (154)
93	Korean Genome Project	NC_000001.11 - 927744	Apr 25, 2020 (154)
94	Northern Sweden	NC_000001.10 - 863124	Jul 12, 2019 (153)
95	Qatari	NC_000001.10 - 863124	Apr 25, 2020 (154)
96	SGDP_PRJ	NC_000001.10 - 863124	Apr 25, 2020 (154)
97	Siberian	NC_000001.10 - 863124	Apr 25, 2020 (154)
98	8.3KJPN	NC_000001.10 - 863124	Apr 25, 2021 (155)
99	14KJPN	NC_000001.11 - 927744	Oct 12, 2022 (156)
100	TopMed	NC_000001.11 - 927744	Apr 25, 2021 (155)
101	UK 10K study - Twins	NC_000001.10 - 863124	Oct 11, 2018 (152)
102	A Vietnamese Genetic Variation Database	NC_000001.10 - 863124	Jul 12, 2019 (153)
103	ALFA	NC_000001.11 - 927744	Apr 25, 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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss78647336	NC_000001.8:902986:G:T	NC_000001.11:927743:G:T	(self)
ss87156742, ss107938340, ss109938360, ss118438913, ss162981395, ss163703654, ss165981272, ss197886320, ss205234590, ss252865278, ss275681737, ss283987785, ss290494007, ss1584130058, ss1712305475, ss3642746691	NC_000001.9:852986:G:T	NC_000001.11:927743:G:T	(self)
7209, 1419, 500, 1358635, 1071, 17453, 1867, 3520, 15049, 1710, 26042, 1419, 317, ss218190974, ss230395858, ss238115431, ss537212515, ss553711183, ss647517080, ss974770152, ss1067612707, ss1289342348, ss1425685220, ss1573851401, ss1599379347, ss1642373380, ss1793710023, ss1917961590, ss2019498806, ss2147485356, ss2624264967, ss2697376297, ss2750648949, ss2986151001, ss3343273217, ss3626006638, ss3637732385, ss3654262252, ss3726717002, ss3745721868, ss3783302537, ss3788980200, ss3793852760, ss3825981763, ss3836378587, ss3847998069, ss3892840059, ss4016889054, ss5142056735, ss5316188156, ss5624751401, ss5831419721, ss5936584013	NC_000001.10:863123:G:T	NC_000001.11:927743:G:T	(self)
18080, 86272, 101, 9573, 34649, 63385, 3467738941, ss2159370397, ss3023513863, ss3646581402, ss3685993617, ss3798744555, ss3841782606, ss3943631572, ss4436457050, ss5240866367, ss5442114169, ss5512492145, ss5666197545, ss5800244635, ss5848749115, ss5906707149	NC_000001.11:927743:G:T	NC_000001.11:927743:G:T	(self)
ss5397733, ss5956368, ss22883050, ss41345645, ss75010777, ss97913351, ss105111861, ss119469535, ss137753523, ss138874237, ss173681055	NT_004350.19:341755:G:T	NC_000001.11:927743:G:T	(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 rs4040604

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

rs4040604