Name: rs6514065
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.

rs6514065

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr20:45868180 (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: C>G
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.429706 (113739/264690, TOPMED)
C=0.424446 (59386/139914, GnomAD)
C=0.43443 (12276/28258, 14KJPN) (+ 16 more)
C=0.40529 (7656/18890, ALFA)
C=0.43234 (7246/16760, 8.3KJPN)
C=0.4344 (2782/6404, 1000G_30x)
C=0.4311 (2159/5008, 1000G)
C=0.3788 (1697/4480, Estonian)
C=0.3812 (1469/3854, ALSPAC)
C=0.3905 (1448/3708, TWINSUK)
C=0.4481 (1313/2930, KOREAN)
C=0.4587 (867/1890, HapMap)
C=0.387 (386/998, GoNL)
C=0.452 (271/600, NorthernSweden)
C=0.264 (121/458, SGDP_PRJ)
G=0.440 (95/216, Qatari)
C=0.448 (95/212, Vietnamese)
C=0.28 (14/50, Siberian)
C=0.28 (11/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ZSWIM3 : 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	18890	C=0.40529	G=0.59471
European	Sub	14286	C=0.38282	G=0.61718
African	Sub	2946	C=0.5309	G=0.4691
African Others	Sub	114	C=0.518	G=0.482
African American	Sub	2832	C=0.5314	G=0.4686
Asian	Sub	112	C=0.536	G=0.464
East Asian	Sub	86	C=0.49	G=0.51
Other Asian	Sub	26	C=0.69	G=0.31
Latin American 1	Sub	146	C=0.390	G=0.610
Latin American 2	Sub	610	C=0.339	G=0.661
South Asian	Sub	98	C=0.42	G=0.58
Other	Sub	692	C=0.373	G=0.627

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	C=0.429706	G=0.570294
gnomAD - Genomes	Global	Study-wide	139914	C=0.424446	G=0.575554
gnomAD - Genomes	European	Sub	75834	C=0.38012	G=0.61988
gnomAD - Genomes	African	Sub	41900	C=0.52468	G=0.47532
gnomAD - Genomes	American	Sub	13590	C=0.33981	G=0.66019
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	C=0.4846	G=0.5154
gnomAD - Genomes	East Asian	Sub	3120	C=0.4679	G=0.5321
gnomAD - Genomes	Other	Sub	2148	C=0.4134	G=0.5866
14KJPN	JAPANESE	Study-wide	28258	C=0.43443	G=0.56557
Allele Frequency Aggregator	Total	Global	18890	C=0.40529	G=0.59471
Allele Frequency Aggregator	European	Sub	14286	C=0.38282	G=0.61718
Allele Frequency Aggregator	African	Sub	2946	C=0.5309	G=0.4691
Allele Frequency Aggregator	Other	Sub	692	C=0.373	G=0.627
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.339	G=0.661
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.390	G=0.610
Allele Frequency Aggregator	Asian	Sub	112	C=0.536	G=0.464
Allele Frequency Aggregator	South Asian	Sub	98	C=0.42	G=0.58
8.3KJPN	JAPANESE	Study-wide	16760	C=0.43234	G=0.56766
1000Genomes_30x	Global	Study-wide	6404	C=0.4344	G=0.5656
1000Genomes_30x	African	Sub	1786	C=0.5498	G=0.4502
1000Genomes_30x	Europe	Sub	1266	C=0.4115	G=0.5885
1000Genomes_30x	South Asian	Sub	1202	C=0.3769	G=0.6231
1000Genomes_30x	East Asian	Sub	1170	C=0.4427	G=0.5573
1000Genomes_30x	American	Sub	980	C=0.314	G=0.686
1000Genomes	Global	Study-wide	5008	C=0.4311	G=0.5689
1000Genomes	African	Sub	1322	C=0.5499	G=0.4501
1000Genomes	East Asian	Sub	1008	C=0.4395	G=0.5605
1000Genomes	Europe	Sub	1006	C=0.4036	G=0.5964
1000Genomes	South Asian	Sub	978	C=0.372	G=0.628
1000Genomes	American	Sub	694	C=0.316	G=0.684
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.3788	G=0.6212
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.3812	G=0.6188
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.3905	G=0.6095
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.4481	G=0.5519
HapMap	Global	Study-wide	1890	C=0.4587	G=0.5413
HapMap	American	Sub	768	C=0.409	G=0.591
HapMap	African	Sub	692	C=0.553	G=0.447
HapMap	Asian	Sub	254	C=0.413	G=0.587
HapMap	Europe	Sub	176	C=0.369	G=0.631
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.387	G=0.613
Northern Sweden	ACPOP	Study-wide	600	C=0.452	G=0.548
SGDP_PRJ	Global	Study-wide	458	C=0.264	G=0.736
Qatari	Global	Study-wide	216	C=0.560	G=0.440
A Vietnamese Genetic Variation Database	Global	Study-wide	212	C=0.448	G=0.552
Siberian	Global	Study-wide	50	C=0.28	G=0.72
The Danish reference pan genome	Danish	Study-wide	40	C=0.28	G=0.72

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 20	NC_000020.11:g.45868180C>G
GRCh37.p13 chr 20	NC_000020.10:g.44496819C>G

Gene: ZSWIM3, zinc finger SWIM-type containing 3 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ZSWIM3 transcript variant 1	NM_080752.4:c.156-8534C>G	N/A	Intron Variant
ZSWIM3 transcript variant 2	NR_037628.2:n.	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	C=	G
GRCh38.p14 chr 20	NC_000020.11:g.45868180=	NC_000020.11:g.45868180C>G
GRCh37.p13 chr 20	NC_000020.10:g.44496819=	NC_000020.10:g.44496819C>G
ZSWIM3 transcript variant 1	NM_080752.3:c.156-8534=	NM_080752.3:c.156-8534C>G
ZSWIM3 transcript variant 1	NM_080752.4:c.156-8534=	NM_080752.4:c.156-8534C>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#.

81 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCM_SSAHASNP	ss10964933	Jul 11, 2003 (116)
2	WI_SSAHASNP	ss12491925	Jul 11, 2003 (116)
3	SC_SNP	ss14742780	Dec 05, 2003 (119)
4	PERLEGEN	ss24083641	Sep 20, 2004 (123)
5	ABI	ss43535885	Mar 15, 2006 (126)
6	AFFY	ss66036979	Jul 04, 2010 (132)
7	CSHL-HAPMAP	ss68396011	Jan 12, 2007 (127)
8	PERLEGEN	ss69242557	May 18, 2007 (127)
9	AFFY	ss75926698	Dec 07, 2007 (129)
10	HGSV	ss77234433	Dec 07, 2007 (129)
11	KRIBB_YJKIM	ss82252710	Dec 15, 2007 (130)
12	BCMHGSC_JDW	ss91709400	Mar 24, 2008 (129)
13	HUMANGENOME_JCVI	ss96231400	Feb 05, 2009 (130)
14	BGI	ss103760868	Dec 01, 2009 (131)
15	1000GENOMES	ss112024947	Jan 25, 2009 (130)
16	1000GENOMES	ss113380495	Jan 25, 2009 (130)
17	ILLUMINA-UK	ss117557769	Feb 14, 2009 (130)
18	ENSEMBL	ss133052191	Dec 01, 2009 (131)
19	ENSEMBL	ss138249207	Dec 01, 2009 (131)
20	AFFY	ss169221621	Jul 04, 2010 (132)
21	COMPLETE_GENOMICS	ss169714144	Jul 04, 2010 (132)
22	COMPLETE_GENOMICS	ss172115891	Jul 04, 2010 (132)
23	BUSHMAN	ss203900586	Jul 04, 2010 (132)
24	BCM-HGSC-SUB	ss208664907	Jul 04, 2010 (132)
25	1000GENOMES	ss228372881	Jul 14, 2010 (132)
26	1000GENOMES	ss237845933	Jul 15, 2010 (132)
27	1000GENOMES	ss244014015	Jul 15, 2010 (132)
28	BL	ss255666784	May 09, 2011 (134)
29	GMI	ss283394511	May 04, 2012 (137)
30	GMI	ss287463198	Apr 25, 2013 (138)
31	PJP	ss292659980	May 09, 2011 (134)
32	TISHKOFF	ss566274473	Apr 25, 2013 (138)
33	SSMP	ss662156194	Apr 25, 2013 (138)
34	EVA-GONL	ss994764403	Aug 21, 2014 (142)
35	JMKIDD_LAB	ss1082235364	Aug 21, 2014 (142)
36	1000GENOMES	ss1364945492	Aug 21, 2014 (142)
37	DDI	ss1429065943	Apr 01, 2015 (144)
38	EVA_GENOME_DK	ss1579521981	Apr 01, 2015 (144)
39	EVA_UK10K_ALSPAC	ss1638873349	Apr 01, 2015 (144)
40	EVA_UK10K_TWINSUK	ss1681867382	Apr 01, 2015 (144)
41	EVA_DECODE	ss1698824996	Apr 01, 2015 (144)
42	EVA_SVP	ss1713697087	Apr 01, 2015 (144)
43	HAMMER_LAB	ss1809520078	Sep 08, 2015 (146)
44	WEILL_CORNELL_DGM	ss1938278564	Feb 12, 2016 (147)
45	GENOMED	ss1969141275	Jul 19, 2016 (147)
46	JJLAB	ss2029919313	Sep 14, 2016 (149)
47	USC_VALOUEV	ss2158487108	Dec 20, 2016 (150)
48	HUMAN_LONGEVITY	ss2243120353	Dec 20, 2016 (150)
49	GRF	ss2704179822	Nov 08, 2017 (151)
50	GNOMAD	ss2967918338	Nov 08, 2017 (151)
51	SWEGEN	ss3018251479	Nov 08, 2017 (151)
52	BIOINF_KMB_FNS_UNIBA	ss3028792388	Nov 08, 2017 (151)
53	CSHL	ss3352529399	Nov 08, 2017 (151)
54	URBANLAB	ss3651027944	Oct 12, 2018 (152)
55	EGCUT_WGS	ss3684938345	Jul 13, 2019 (153)
56	EVA_DECODE	ss3707031465	Jul 13, 2019 (153)
57	ACPOP	ss3743429539	Jul 13, 2019 (153)
58	EVA	ss3758696571	Jul 13, 2019 (153)
59	PACBIO	ss3788658555	Jul 13, 2019 (153)
60	PACBIO	ss3793548023	Jul 13, 2019 (153)
61	PACBIO	ss3798434982	Jul 13, 2019 (153)
62	KHV_HUMAN_GENOMES	ss3821856847	Jul 13, 2019 (153)
63	EVA	ss3835693177	Apr 27, 2020 (154)
64	EVA	ss3841470538	Apr 27, 2020 (154)
65	EVA	ss3846983457	Apr 27, 2020 (154)
66	SGDP_PRJ	ss3889191443	Apr 27, 2020 (154)
67	KRGDB	ss3939489286	Apr 27, 2020 (154)
68	TOPMED	ss5090148607	Apr 26, 2021 (155)
69	TOMMO_GENOMICS	ss5229846632	Apr 26, 2021 (155)
70	1000G_HIGH_COVERAGE	ss5308951432	Oct 16, 2022 (156)
71	EVA	ss5437688333	Oct 16, 2022 (156)
72	HUGCELL_USP	ss5501215166	Oct 16, 2022 (156)
73	EVA	ss5512230295	Oct 16, 2022 (156)
74	1000G_HIGH_COVERAGE	ss5615486968	Oct 16, 2022 (156)
75	SANFORD_IMAGENETICS	ss5663297655	Oct 16, 2022 (156)
76	TOMMO_GENOMICS	ss5789706563	Oct 16, 2022 (156)
77	YY_MCH	ss5818081102	Oct 16, 2022 (156)
78	EVA	ss5845752768	Oct 16, 2022 (156)
79	EVA	ss5853158276	Oct 16, 2022 (156)
80	EVA	ss5923604516	Oct 16, 2022 (156)
81	EVA	ss5958219879	Oct 16, 2022 (156)
82	1000Genomes	NC_000020.10 - 44496819	Oct 12, 2018 (152)
83	1000Genomes_30x	NC_000020.11 - 45868180	Oct 16, 2022 (156)
84	The Avon Longitudinal Study of Parents and Children	NC_000020.10 - 44496819	Oct 12, 2018 (152)
85	Genetic variation in the Estonian population	NC_000020.10 - 44496819	Oct 12, 2018 (152)
86	The Danish reference pan genome	NC_000020.10 - 44496819	Apr 27, 2020 (154)
87	gnomAD - Genomes	NC_000020.11 - 45868180	Apr 26, 2021 (155)
88	Genome of the Netherlands Release 5	NC_000020.10 - 44496819	Apr 27, 2020 (154)
89	HapMap	NC_000020.11 - 45868180	Apr 27, 2020 (154)
90	KOREAN population from KRGDB	NC_000020.10 - 44496819	Apr 27, 2020 (154)
91	Northern Sweden	NC_000020.10 - 44496819	Jul 13, 2019 (153)
92	Qatari	NC_000020.10 - 44496819	Apr 27, 2020 (154)
93	SGDP_PRJ	NC_000020.10 - 44496819	Apr 27, 2020 (154)
94	Siberian	NC_000020.10 - 44496819	Apr 27, 2020 (154)
95	8.3KJPN	NC_000020.10 - 44496819	Apr 26, 2021 (155)
96	14KJPN	NC_000020.11 - 45868180	Oct 16, 2022 (156)
97	TopMed	NC_000020.11 - 45868180	Apr 26, 2021 (155)
98	UK 10K study - Twins	NC_000020.10 - 44496819	Oct 12, 2018 (152)
99	A Vietnamese Genetic Variation Database	NC_000020.10 - 44496819	Jul 13, 2019 (153)
100	ALFA	NC_000020.11 - 45868180	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)
rs58236288	Feb 27, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss75926698, ss77234433, ss91709400, ss112024947, ss113380495, ss117557769, ss169221621, ss169714144, ss172115891, ss203900586, ss208664907, ss255666784, ss283394511, ss287463198, ss292659980, ss1698824996, ss1713697087	NC_000020.9:43930225:C:G	NC_000020.11:45868179:C:G	(self)
78414708, 43409853, 30676593, 5686920, 19336173, 46666680, 16714404, 20320486, 41208423, 11003462, 87815939, 43409853, 9576522, ss228372881, ss237845933, ss244014015, ss566274473, ss662156194, ss994764403, ss1082235364, ss1364945492, ss1429065943, ss1579521981, ss1638873349, ss1681867382, ss1809520078, ss1938278564, ss1969141275, ss2029919313, ss2158487108, ss2704179822, ss2967918338, ss3018251479, ss3352529399, ss3684938345, ss3743429539, ss3758696571, ss3788658555, ss3793548023, ss3798434982, ss3835693177, ss3841470538, ss3889191443, ss3939489286, ss5229846632, ss5437688333, ss5512230295, ss5663297655, ss5845752768, ss5958219879	NC_000020.10:44496818:C:G	NC_000020.11:45868179:C:G	(self)
103012903, 553124153, 2131951, 123543667, 365257552, 1451564279, ss2243120353, ss3028792388, ss3651027944, ss3707031465, ss3821856847, ss3846983457, ss5090148607, ss5308951432, ss5501215166, ss5615486968, ss5789706563, ss5818081102, ss5853158276, ss5923604516	NC_000020.11:45868179:C:G	NC_000020.11:45868179:C:G	(self)
ss10964933, ss12491925, ss14742780	NT_011362.8:9549726:C:G	NC_000020.11:45868179:C:G	(self)
ss24083641, ss43535885, ss68396011, ss69242557, ss82252710, ss96231400, ss103760868, ss133052191, ss138249207	NT_011362.10:14692910:C:G	NC_000020.11:45868179:C:G	(self)
ss66036979	NT_011362.11:14816671:C:G	NC_000020.11:45868179:C: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 rs6514065

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

rs6514065