Name: rs1006798
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.

rs1006798

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:3256646 (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: A>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.294945 (78069/264690, TOPMED)
G=0.317203 (44442/140106, GnomAD)
G=0.33446 (19564/58494, ALFA) (+ 18 more)
G=0.38616 (10912/28258, 14KJPN)
G=0.38574 (6465/16760, 8.3KJPN)
G=0.2762 (1769/6404, 1000G_30x)
G=0.2782 (1393/5008, 1000G)
G=0.4154 (1861/4480, Estonian)
G=0.3757 (1448/3854, ALSPAC)
G=0.3781 (1402/3708, TWINSUK)
G=0.4218 (1236/2930, KOREAN)
G=0.4269 (782/1832, Korea1K)
G=0.375 (374/998, GoNL)
G=0.378 (298/788, PRJEB37584)
G=0.438 (263/600, NorthernSweden)
G=0.274 (90/328, HapMap)
A=0.372 (105/282, SGDP_PRJ)
G=0.157 (34/216, Qatari)
G=0.314 (66/210, Vietnamese)
A=0.38 (16/42, Siberian)
G=0.28 (11/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: MSANTD1 : 500B Downstream 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	58494	A=0.66554	G=0.33446
European	Sub	43028	A=0.64514	G=0.35486
African	Sub	5132	A=0.8127	G=0.1873
African Others	Sub	190	A=0.805	G=0.195
African American	Sub	4942	A=0.8130	G=0.1870
Asian	Sub	450	A=0.638	G=0.362
East Asian	Sub	384	A=0.635	G=0.365
Other Asian	Sub	66	A=0.65	G=0.35
Latin American 1	Sub	588	A=0.733	G=0.267
Latin American 2	Sub	4968	A=0.6872	G=0.3128
South Asian	Sub	178	A=0.792	G=0.208
Other	Sub	4150	A=0.6571	G=0.3429

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	A=0.705055	G=0.294945
gnomAD - Genomes	Global	Study-wide	140106	A=0.682797	G=0.317203
gnomAD - Genomes	European	Sub	75866	A=0.60923	G=0.39077
gnomAD - Genomes	African	Sub	42002	A=0.81249	G=0.18751
gnomAD - Genomes	American	Sub	13642	A=0.70708	G=0.29292
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	A=0.6515	G=0.3485
gnomAD - Genomes	East Asian	Sub	3126	A=0.6347	G=0.3653
gnomAD - Genomes	Other	Sub	2150	A=0.7093	G=0.2907
Allele Frequency Aggregator	Total	Global	58494	A=0.66554	G=0.33446
Allele Frequency Aggregator	European	Sub	43028	A=0.64514	G=0.35486
Allele Frequency Aggregator	African	Sub	5132	A=0.8127	G=0.1873
Allele Frequency Aggregator	Latin American 2	Sub	4968	A=0.6872	G=0.3128
Allele Frequency Aggregator	Other	Sub	4150	A=0.6571	G=0.3429
Allele Frequency Aggregator	Latin American 1	Sub	588	A=0.733	G=0.267
Allele Frequency Aggregator	Asian	Sub	450	A=0.638	G=0.362
Allele Frequency Aggregator	South Asian	Sub	178	A=0.792	G=0.208
14KJPN	JAPANESE	Study-wide	28258	A=0.61384	G=0.38616
8.3KJPN	JAPANESE	Study-wide	16760	A=0.61426	G=0.38574
1000Genomes_30x	Global	Study-wide	6404	A=0.7238	G=0.2762
1000Genomes_30x	African	Sub	1786	A=0.8488	G=0.1512
1000Genomes_30x	Europe	Sub	1266	A=0.6256	G=0.3744
1000Genomes_30x	South Asian	Sub	1202	A=0.7346	G=0.2654
1000Genomes_30x	East Asian	Sub	1170	A=0.6632	G=0.3368
1000Genomes_30x	American	Sub	980	A=0.682	G=0.318
1000Genomes	Global	Study-wide	5008	A=0.7218	G=0.2782
1000Genomes	African	Sub	1322	A=0.8472	G=0.1528
1000Genomes	East Asian	Sub	1008	A=0.6647	G=0.3353
1000Genomes	Europe	Sub	1006	A=0.6193	G=0.3807
1000Genomes	South Asian	Sub	978	A=0.743	G=0.257
1000Genomes	American	Sub	694	A=0.684	G=0.316
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.5846	G=0.4154
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.6243	G=0.3757
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.6219	G=0.3781
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.5782	G=0.4218
Korean Genome Project	KOREAN	Study-wide	1832	A=0.5731	G=0.4269
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.625	G=0.375
CNV burdens in cranial meningiomas	Global	Study-wide	788	A=0.622	G=0.378
CNV burdens in cranial meningiomas	CRM	Sub	788	A=0.622	G=0.378
Northern Sweden	ACPOP	Study-wide	600	A=0.562	G=0.438
HapMap	Global	Study-wide	328	A=0.726	G=0.274
HapMap	African	Sub	120	A=0.858	G=0.142
HapMap	American	Sub	120	A=0.642	G=0.358
HapMap	Asian	Sub	88	A=0.66	G=0.34
SGDP_PRJ	Global	Study-wide	282	A=0.372	G=0.628
Qatari	Global	Study-wide	216	A=0.843	G=0.157
A Vietnamese Genetic Variation Database	Global	Study-wide	210	A=0.686	G=0.314
Siberian	Global	Study-wide	42	A=0.38	G=0.62
The Danish reference pan genome	Danish	Study-wide	40	A=0.72	G=0.28

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 4	NC_000004.12:g.3256646A>G
GRCh37.p13 chr 4	NC_000004.11:g.3258373A>G

Gene: MSANTD1, Myb/SANT DNA binding domain containing 1 (plus strand) : 500B Downstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
MSANTD1 transcript variant 1	NM_001042690.2:c.	N/A	Downstream Transcript Variant
MSANTD1 transcript variant 2	NM_001330620.2:c.	N/A	Downstream Transcript Variant
MSANTD1 transcript variant X1	XM_011513467.4:c.	N/A	Downstream Transcript Variant
MSANTD1 transcript variant X2	XM_047415655.1:c.	N/A	Downstream Transcript 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	A=	G
GRCh38.p14 chr 4	NC_000004.12:g.3256646=	NC_000004.12:g.3256646A>G
GRCh37.p13 chr 4	NC_000004.11:g.3258373=	NC_000004.11:g.3258373A>G

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, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss1468781	Oct 05, 2000 (86)
2	SC_JCM	ss4383199	Mar 26, 2002 (103)
3	ABI	ss44495747	Mar 15, 2006 (126)
4	BCMHGSC_JDW	ss92442549	Mar 23, 2008 (129)
5	HUMANGENOME_JCVI	ss98927006	Feb 04, 2009 (130)
6	BGI	ss104033067	Dec 01, 2009 (131)
7	1000GENOMES	ss112854564	Jan 25, 2009 (130)
8	ENSEMBL	ss133351310	Dec 01, 2009 (131)
9	ENSEMBL	ss139400155	Dec 01, 2009 (131)
10	GMI	ss156757533	Dec 01, 2009 (131)
11	ILLUMINA	ss159858803	Dec 01, 2009 (131)
12	COMPLETE_GENOMICS	ss166016039	Jul 04, 2010 (132)
13	BUSHMAN	ss197915606	Jul 04, 2010 (132)
14	1000GENOMES	ss211345157	Jul 14, 2010 (132)
15	1000GENOMES	ss220699766	Jul 14, 2010 (132)
16	1000GENOMES	ss232229270	Jul 14, 2010 (132)
17	1000GENOMES	ss239557357	Jul 15, 2010 (132)
18	GMI	ss277542787	May 04, 2012 (137)
19	GMI	ss284831093	Apr 25, 2013 (138)
20	PJP	ss293055864	May 09, 2011 (134)
21	ILLUMINA	ss479501696	Sep 08, 2015 (146)
22	ILLUMINA	ss483539219	May 04, 2012 (137)
23	ILLUMINA	ss484804464	May 04, 2012 (137)
24	TISHKOFF	ss557261907	Apr 25, 2013 (138)
25	SSMP	ss651016102	Apr 25, 2013 (138)
26	ILLUMINA	ss780315561	Aug 21, 2014 (142)
27	ILLUMINA	ss782213148	Aug 21, 2014 (142)
28	ILLUMINA	ss835802603	Aug 21, 2014 (142)
29	EVA-GONL	ss979685435	Aug 21, 2014 (142)
30	JMKIDD_LAB	ss1071222788	Aug 21, 2014 (142)
31	1000GENOMES	ss1308140441	Aug 21, 2014 (142)
32	DDI	ss1429743367	Apr 01, 2015 (144)
33	EVA_GENOME_DK	ss1580384461	Apr 01, 2015 (144)
34	EVA_DECODE	ss1589181640	Apr 01, 2015 (144)
35	EVA_UK10K_ALSPAC	ss1609263078	Apr 01, 2015 (144)
36	EVA_UK10K_TWINSUK	ss1652257111	Apr 01, 2015 (144)
37	WEILL_CORNELL_DGM	ss1922916990	Feb 12, 2016 (147)
38	GENOMED	ss1969639509	Jul 19, 2016 (147)
39	JJLAB	ss2022032043	Sep 14, 2016 (149)
40	USC_VALOUEV	ss2150138832	Dec 20, 2016 (150)
41	HUMAN_LONGEVITY	ss2259936615	Dec 20, 2016 (150)
42	SYSTEMSBIOZJU	ss2625516639	Nov 08, 2017 (151)
43	ILLUMINA	ss2634072325	Nov 08, 2017 (151)
44	GRF	ss2705573478	Nov 08, 2017 (151)
45	GNOMAD	ss2804839383	Nov 08, 2017 (151)
46	SWEGEN	ss2994013420	Nov 08, 2017 (151)
47	BIOINF_KMB_FNS_UNIBA	ss3024785333	Nov 08, 2017 (151)
48	CSHL	ss3345503862	Nov 08, 2017 (151)
49	ILLUMINA	ss3632011747	Oct 12, 2018 (152)
50	ILLUMINA	ss3636636413	Oct 12, 2018 (152)
51	ILLUMINA	ss3642311808	Oct 12, 2018 (152)
52	OMUKHERJEE_ADBS	ss3646300543	Oct 12, 2018 (152)
53	URBANLAB	ss3647634638	Oct 12, 2018 (152)
54	EGCUT_WGS	ss3661952262	Jul 13, 2019 (153)
55	EVA_DECODE	ss3711263207	Jul 13, 2019 (153)
56	ACPOP	ss3730788752	Jul 13, 2019 (153)
57	EVA	ss3761301434	Jul 13, 2019 (153)
58	PACBIO	ss3784597821	Jul 13, 2019 (153)
59	PACBIO	ss3790070850	Jul 13, 2019 (153)
60	PACBIO	ss3794945923	Jul 13, 2019 (153)
61	KHV_HUMAN_GENOMES	ss3804439282	Jul 13, 2019 (153)
62	EVA	ss3825652347	Apr 25, 2020 (154)
63	EVA	ss3828332732	Apr 25, 2020 (154)
64	EVA	ss3837596431	Apr 25, 2020 (154)
65	EVA	ss3843029893	Apr 25, 2020 (154)
66	SGDP_PRJ	ss3858051025	Apr 25, 2020 (154)
67	KRGDB	ss3904185306	Apr 25, 2020 (154)
68	KOGIC	ss3953383513	Apr 25, 2020 (154)
69	EVA	ss3984522489	Apr 26, 2021 (155)
70	TOPMED	ss4600623001	Apr 26, 2021 (155)
71	TOMMO_GENOMICS	ss5163881927	Apr 26, 2021 (155)
72	1000G_HIGH_COVERAGE	ss5257789769	Oct 13, 2022 (156)
73	EVA	ss5314929329	Oct 13, 2022 (156)
74	EVA	ss5346458205	Oct 13, 2022 (156)
75	HUGCELL_USP	ss5456737333	Oct 13, 2022 (156)
76	1000G_HIGH_COVERAGE	ss5538110103	Oct 13, 2022 (156)
77	SANFORD_IMAGENETICS	ss5634198468	Oct 13, 2022 (156)
78	TOMMO_GENOMICS	ss5697439937	Oct 13, 2022 (156)
79	YY_MCH	ss5804688410	Oct 13, 2022 (156)
80	EVA	ss5843446649	Oct 13, 2022 (156)
81	EVA	ss5854050654	Oct 13, 2022 (156)
82	EVA	ss5861869396	Oct 13, 2022 (156)
83	EVA	ss5962574176	Oct 13, 2022 (156)
84	1000Genomes	NC_000004.11 - 3258373	Oct 12, 2018 (152)
85	1000Genomes_30x	NC_000004.12 - 3256646	Oct 13, 2022 (156)
86	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 3258373	Oct 12, 2018 (152)
87	Genetic variation in the Estonian population	NC_000004.11 - 3258373	Oct 12, 2018 (152)
88	The Danish reference pan genome	NC_000004.11 - 3258373	Apr 25, 2020 (154)
89	gnomAD - Genomes	NC_000004.12 - 3256646	Apr 26, 2021 (155)
90	Genome of the Netherlands Release 5	NC_000004.11 - 3258373	Apr 25, 2020 (154)
91	HapMap	NC_000004.12 - 3256646	Apr 25, 2020 (154)
92	KOREAN population from KRGDB	NC_000004.11 - 3258373	Apr 25, 2020 (154)
93	Korean Genome Project	NC_000004.12 - 3256646	Apr 25, 2020 (154)
94	Northern Sweden	NC_000004.11 - 3258373	Jul 13, 2019 (153)
95	CNV burdens in cranial meningiomas	NC_000004.11 - 3258373	Apr 26, 2021 (155)
96	Qatari	NC_000004.11 - 3258373	Apr 25, 2020 (154)
97	SGDP_PRJ	NC_000004.11 - 3258373	Apr 25, 2020 (154)
98	Siberian	NC_000004.11 - 3258373	Apr 25, 2020 (154)
99	8.3KJPN	NC_000004.11 - 3258373	Apr 26, 2021 (155)
100	14KJPN	NC_000004.12 - 3256646	Oct 13, 2022 (156)
101	TopMed	NC_000004.12 - 3256646	Apr 26, 2021 (155)
102	UK 10K study - Twins	NC_000004.11 - 3258373	Oct 12, 2018 (152)
103	A Vietnamese Genetic Variation Database	NC_000004.11 - 3258373	Jul 13, 2019 (153)
104	ALFA	NC_000004.12 - 3256646	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss92442549, ss112854564, ss159858803, ss166016039, ss197915606, ss211345157, ss277542787, ss284831093, ss293055864, ss484804464, ss1589181640	NC_000004.10:3228170:A:G	NC_000004.12:3256645:A:G	(self)
19480062, 10857699, 7690510, 6549400, 4770558, 11362700, 4073617, 71847, 4958920, 10068005, 2655186, 21851234, 10857699, 2372493, ss220699766, ss232229270, ss239557357, ss479501696, ss483539219, ss557261907, ss651016102, ss780315561, ss782213148, ss835802603, ss979685435, ss1071222788, ss1308140441, ss1429743367, ss1580384461, ss1609263078, ss1652257111, ss1922916990, ss1969639509, ss2022032043, ss2150138832, ss2625516639, ss2634072325, ss2705573478, ss2804839383, ss2994013420, ss3345503862, ss3632011747, ss3636636413, ss3642311808, ss3646300543, ss3661952262, ss3730788752, ss3761301434, ss3784597821, ss3790070850, ss3794945923, ss3825652347, ss3828332732, ss3837596431, ss3858051025, ss3904185306, ss3984522489, ss5163881927, ss5314929329, ss5346458205, ss5634198468, ss5843446649, ss5962574176	NC_000004.11:3258372:A:G	NC_000004.12:3256645:A:G	(self)
25636038, 138300418, 2544751, 9761514, 31277041, 438000557, 7344094079, ss2259936615, ss3024785333, ss3647634638, ss3711263207, ss3804439282, ss3843029893, ss3953383513, ss4600623001, ss5257789769, ss5456737333, ss5538110103, ss5697439937, ss5804688410, ss5854050654, ss5861869396	NC_000004.12:3256645:A:G	NC_000004.12:3256645:A:G	(self)
ss1468781, ss4383199, ss44495747, ss98927006, ss104033067, ss133351310, ss139400155, ss156757533	NT_006051.18:1779726:A:G	NC_000004.12:3256645:A: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 rs1006798

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs1006798