Name: rs29939
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.

rs29939

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr19:33819895 (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: A=0.299841 (79365/264690, TOPMED)
A=0.293351 (41109/140136, GnomAD)
A=0.31298 (29911/95568, ALFA) (+ 15 more)
G=0.21491 (6073/28258, 14KJPN)
G=0.21432 (3592/16760, 8.3KJPN)
A=0.3812 (2441/6404, 1000G_30x)
A=0.3882 (1944/5008, 1000G)
A=0.3417 (1531/4480, Estonian)
A=0.3168 (1221/3854, ALSPAC)
A=0.3347 (1241/3708, TWINSUK)
G=0.2208 (647/2930, KOREAN)
G=0.2104 (380/1806, Korea1K)
A=0.367 (220/600, NorthernSweden)
A=0.263 (114/434, SGDP_PRJ)
A=0.363 (119/328, HapMap)
A=0.361 (78/216, Qatari)
A=0.31 (13/42, Siberian)
A=0.33 (13/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: None
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	95568	A=0.31298	G=0.68702
European	Sub	78182	A=0.31841	G=0.68159
African	Sub	7572	A=0.1730	G=0.8270
African Others	Sub	264	A=0.106	G=0.894
African American	Sub	7308	A=0.1754	G=0.8246
Asian	Sub	430	A=0.777	G=0.223
East Asian	Sub	366	A=0.773	G=0.227
Other Asian	Sub	64	A=0.80	G=0.20
Latin American 1	Sub	572	A=0.276	G=0.724
Latin American 2	Sub	4854	A=0.4042	G=0.5958
South Asian	Sub	164	A=0.329	G=0.671
Other	Sub	3794	A=0.3160	G=0.6840

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=0.299841	G=0.700159
gnomAD - Genomes	Global	Study-wide	140136	A=0.293351	G=0.706649
gnomAD - Genomes	European	Sub	75854	A=0.32694	G=0.67306
gnomAD - Genomes	African	Sub	42028	A=0.18024	G=0.81976
gnomAD - Genomes	American	Sub	13656	A=0.34644	G=0.65356
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	A=0.2574	G=0.7426
gnomAD - Genomes	East Asian	Sub	3126	A=0.7761	G=0.2239
gnomAD - Genomes	Other	Sub	2150	A=0.3358	G=0.6642
Allele Frequency Aggregator	Total	Global	95568	A=0.31298	G=0.68702
Allele Frequency Aggregator	European	Sub	78182	A=0.31841	G=0.68159
Allele Frequency Aggregator	African	Sub	7572	A=0.1730	G=0.8270
Allele Frequency Aggregator	Latin American 2	Sub	4854	A=0.4042	G=0.5958
Allele Frequency Aggregator	Other	Sub	3794	A=0.3160	G=0.6840
Allele Frequency Aggregator	Latin American 1	Sub	572	A=0.276	G=0.724
Allele Frequency Aggregator	Asian	Sub	430	A=0.777	G=0.223
Allele Frequency Aggregator	South Asian	Sub	164	A=0.329	G=0.671
14KJPN	JAPANESE	Study-wide	28258	A=0.78509	G=0.21491
8.3KJPN	JAPANESE	Study-wide	16760	A=0.78568	G=0.21432
1000Genomes_30x	Global	Study-wide	6404	A=0.3812	G=0.6188
1000Genomes_30x	African	Sub	1786	A=0.1439	G=0.8561
1000Genomes_30x	Europe	Sub	1266	A=0.3357	G=0.6643
1000Genomes_30x	South Asian	Sub	1202	A=0.3952	G=0.6048
1000Genomes_30x	East Asian	Sub	1170	A=0.7641	G=0.2359
1000Genomes_30x	American	Sub	980	A=0.398	G=0.602
1000Genomes	Global	Study-wide	5008	A=0.3882	G=0.6118
1000Genomes	African	Sub	1322	A=0.1490	G=0.8510
1000Genomes	East Asian	Sub	1008	A=0.7609	G=0.2391
1000Genomes	Europe	Sub	1006	A=0.3320	G=0.6680
1000Genomes	South Asian	Sub	978	A=0.380	G=0.620
1000Genomes	American	Sub	694	A=0.395	G=0.605
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.3417	G=0.6583
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.3168	G=0.6832
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.3347	G=0.6653
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.7792	G=0.2208
Korean Genome Project	KOREAN	Study-wide	1806	A=0.7896	G=0.2104
Northern Sweden	ACPOP	Study-wide	600	A=0.367	G=0.633
SGDP_PRJ	Global	Study-wide	434	A=0.263	G=0.737
HapMap	Global	Study-wide	328	A=0.363	G=0.637
HapMap	African	Sub	120	A=0.092	G=0.908
HapMap	American	Sub	120	A=0.333	G=0.667
HapMap	Asian	Sub	88	A=0.77	G=0.23
Qatari	Global	Study-wide	216	A=0.361	G=0.639
Siberian	Global	Study-wide	42	A=0.31	G=0.69
The Danish reference pan genome	Danish	Study-wide	40	A=0.33	G=0.68

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 19	NC_000019.10:g.33819895A>G
GRCh37.p13 chr 19	NC_000019.9:g.34310800A>G

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 19	NC_000019.10:g.33819895=	NC_000019.10:g.33819895A>G
GRCh37.p13 chr 19	NC_000019.9:g.34310800=	NC_000019.9:g.34310800A>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#.

94 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	KWOK	ss29732	May 08, 2000 (76)
2	KWOK	ss371889	Jul 10, 2000 (79)
3	SC_JCM	ss630772	Jul 16, 2000 (80)
4	KWOK	ss1249279	Oct 04, 2000 (86)
5	TSC-CSHL	ss1307191	Oct 05, 2000 (92)
6	KWOK	ss1966787	Oct 18, 2000 (87)
7	KWOK	ss1974680	Oct 18, 2000 (87)
8	BCM_SSAHASNP	ss10932071	Jul 11, 2003 (116)
9	SSAHASNP	ss21509431	Apr 05, 2004 (121)
10	PERLEGEN	ss24525942	Sep 20, 2004 (123)
11	ABI	ss44196094	Mar 14, 2006 (126)
12	HGSV	ss80516403	Dec 14, 2007 (130)
13	BCMHGSC_JDW	ss90958949	Mar 24, 2008 (129)
14	HUMANGENOME_JCVI	ss96302636	Feb 04, 2009 (130)
15	BGI	ss103435685	Dec 01, 2009 (131)
16	ILLUMINA-UK	ss117692507	Feb 14, 2009 (130)
17	ENSEMBL	ss137653923	Dec 01, 2009 (131)
18	ILLUMINA	ss160605224	Dec 01, 2009 (131)
19	COMPLETE_GENOMICS	ss168134504	Jul 04, 2010 (132)
20	COMPLETE_GENOMICS	ss169611373	Jul 04, 2010 (132)
21	BUSHMAN	ss203741087	Jul 04, 2010 (132)
22	1000GENOMES	ss211958515	Jul 14, 2010 (132)
23	1000GENOMES	ss228121420	Jul 14, 2010 (132)
24	1000GENOMES	ss237663222	Jul 15, 2010 (132)
25	1000GENOMES	ss243871927	Jul 15, 2010 (132)
26	PJP	ss292243046	May 09, 2011 (134)
27	ILLUMINA	ss480736635	May 04, 2012 (137)
28	ILLUMINA	ss480752448	May 04, 2012 (137)
29	ILLUMINA	ss481635345	Sep 08, 2015 (146)
30	ILLUMINA	ss485163021	May 04, 2012 (137)
31	TISHKOFF	ss565957503	Apr 25, 2013 (138)
32	SSMP	ss661818685	Apr 25, 2013 (138)
33	ILLUMINA	ss783027761	Sep 08, 2015 (146)
34	ILLUMINA	ss832285354	Sep 08, 2015 (146)
35	EVA-GONL	ss994256925	Aug 21, 2014 (142)
36	JMKIDD_LAB	ss1081875007	Aug 21, 2014 (142)
37	1000GENOMES	ss1362999355	Aug 21, 2014 (142)
38	DDI	ss1428392007	Apr 01, 2015 (144)
39	EVA_GENOME_DK	ss1578623761	Apr 01, 2015 (144)
40	EVA_UK10K_ALSPAC	ss1637885883	Apr 01, 2015 (144)
41	EVA_UK10K_TWINSUK	ss1680879916	Apr 01, 2015 (144)
42	EVA_DECODE	ss1698309976	Apr 01, 2015 (144)
43	ILLUMINA	ss1752281830	Sep 08, 2015 (146)
44	HAMMER_LAB	ss1809288908	Sep 08, 2015 (146)
45	WEILL_CORNELL_DGM	ss1937750489	Feb 12, 2016 (147)
46	JJLAB	ss2029652412	Sep 14, 2016 (149)
47	USC_VALOUEV	ss2158190786	Dec 20, 2016 (150)
48	HUMAN_LONGEVITY	ss2225436708	Dec 20, 2016 (150)
49	SYSTEMSBIOZJU	ss2629323665	Nov 08, 2017 (151)
50	ILLUMINA	ss2633535162	Nov 08, 2017 (151)
51	GRF	ss2702798971	Nov 08, 2017 (151)
52	GNOMAD	ss2962371357	Nov 08, 2017 (151)
53	AFFY	ss2985139021	Nov 08, 2017 (151)
54	SWEGEN	ss3017397444	Nov 08, 2017 (151)
55	BIOINF_KMB_FNS_UNIBA	ss3028659016	Nov 08, 2017 (151)
56	CSHL	ss3352283329	Nov 08, 2017 (151)
57	ILLUMINA	ss3633889286	Oct 12, 2018 (152)
58	ILLUMINA	ss3634732435	Oct 12, 2018 (152)
59	ILLUMINA	ss3636420577	Oct 12, 2018 (152)
60	ILLUMINA	ss3637327855	Oct 12, 2018 (152)
61	ILLUMINA	ss3640439743	Oct 12, 2018 (152)
62	URBANLAB	ss3650908594	Oct 12, 2018 (152)
63	EGCUT_WGS	ss3684174651	Jul 13, 2019 (153)
64	EVA_DECODE	ss3702681933	Jul 13, 2019 (153)
65	ACPOP	ss3743001172	Jul 13, 2019 (153)
66	ILLUMINA	ss3745032458	Jul 13, 2019 (153)
67	EVA	ss3756013634	Jul 13, 2019 (153)
68	ILLUMINA	ss3772529629	Jul 13, 2019 (153)
69	PACBIO	ss3788518237	Jul 13, 2019 (153)
70	PACBIO	ss3793431156	Jul 13, 2019 (153)
71	PACBIO	ss3798317921	Jul 13, 2019 (153)
72	KHV_HUMAN_GENOMES	ss3821261800	Jul 13, 2019 (153)
73	EVA	ss3835440534	Apr 27, 2020 (154)
74	EVA	ss3841342560	Apr 27, 2020 (154)
75	EVA	ss3846848362	Apr 27, 2020 (154)
76	SGDP_PRJ	ss3888126713	Apr 27, 2020 (154)
77	KRGDB	ss3938214869	Apr 27, 2020 (154)
78	KOGIC	ss3981250282	Apr 27, 2020 (154)
79	EVA	ss4017822596	Apr 26, 2021 (155)
80	TOPMED	ss5073395901	Apr 26, 2021 (155)
81	TOMMO_GENOMICS	ss5227545601	Apr 26, 2021 (155)
82	1000G_HIGH_COVERAGE	ss5307093913	Oct 16, 2022 (156)
83	EVA	ss5434576902	Oct 16, 2022 (156)
84	HUGCELL_USP	ss5499639188	Oct 16, 2022 (156)
85	EVA	ss5512090723	Oct 16, 2022 (156)
86	1000G_HIGH_COVERAGE	ss5612757090	Oct 16, 2022 (156)
87	SANFORD_IMAGENETICS	ss5662307793	Oct 16, 2022 (156)
88	TOMMO_GENOMICS	ss5786107888	Oct 16, 2022 (156)
89	EVA	ss5800007713	Oct 16, 2022 (156)
90	YY_MCH	ss5817561918	Oct 16, 2022 (156)
91	EVA	ss5840491174	Oct 16, 2022 (156)
92	EVA	ss5852272345	Oct 16, 2022 (156)
93	EVA	ss5927939497	Oct 16, 2022 (156)
94	EVA	ss5953723511	Oct 16, 2022 (156)
95	1000Genomes	NC_000019.9 - 34310800	Oct 12, 2018 (152)
96	1000Genomes_30x	NC_000019.10 - 33819895	Oct 16, 2022 (156)
97	The Avon Longitudinal Study of Parents and Children	NC_000019.9 - 34310800	Oct 12, 2018 (152)
98	Genetic variation in the Estonian population	NC_000019.9 - 34310800	Oct 12, 2018 (152)
99	The Danish reference pan genome	NC_000019.9 - 34310800	Apr 27, 2020 (154)
100	gnomAD - Genomes	NC_000019.10 - 33819895	Apr 26, 2021 (155)
101	HapMap	NC_000019.10 - 33819895	Apr 27, 2020 (154)
102	KOREAN population from KRGDB	NC_000019.9 - 34310800	Apr 27, 2020 (154)
103	Korean Genome Project	NC_000019.10 - 33819895	Apr 27, 2020 (154)
104	Northern Sweden	NC_000019.9 - 34310800	Jul 13, 2019 (153)
105	Qatari	NC_000019.9 - 34310800	Apr 27, 2020 (154)
106	SGDP_PRJ	NC_000019.9 - 34310800	Apr 27, 2020 (154)
107	Siberian	NC_000019.9 - 34310800	Apr 27, 2020 (154)
108	8.3KJPN	NC_000019.9 - 34310800	Apr 26, 2021 (155)
109	14KJPN	NC_000019.10 - 33819895	Oct 16, 2022 (156)
110	TopMed	NC_000019.10 - 33819895	Apr 26, 2021 (155)
111	UK 10K study - Twins	NC_000019.9 - 34310800	Oct 12, 2018 (152)
112	ALFA	NC_000019.10 - 33819895	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)
rs880880	Jan 18, 2001 (92)
rs17247930	Oct 08, 2004 (123)
rs57579357	May 23, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss80516403, ss90958949, ss117692507, ss168134504, ss169611373, ss203741087, ss211958515, ss292243046, ss480736635, ss1698309976	NC_000019.8:39002639:A:G	NC_000019.10:33819894:A:G	(self)
76400257, 42317893, 29912899, 4806920, 45392263, 16286037, 19792411, 40143693, 10707140, 85514908, 42317893, ss228121420, ss237663222, ss243871927, ss480752448, ss481635345, ss485163021, ss565957503, ss661818685, ss783027761, ss832285354, ss994256925, ss1081875007, ss1362999355, ss1428392007, ss1578623761, ss1637885883, ss1680879916, ss1752281830, ss1809288908, ss1937750489, ss2029652412, ss2158190786, ss2629323665, ss2633535162, ss2702798971, ss2962371357, ss2985139021, ss3017397444, ss3352283329, ss3633889286, ss3634732435, ss3636420577, ss3637327855, ss3640439743, ss3684174651, ss3743001172, ss3745032458, ss3756013634, ss3772529629, ss3788518237, ss3793431156, ss3798317921, ss3835440534, ss3841342560, ss3888126713, ss3938214869, ss4017822596, ss5227545601, ss5434576902, ss5512090723, ss5662307793, ss5800007713, ss5840491174, ss5953723511	NC_000019.9:34310799:A:G	NC_000019.10:33819894:A:G	(self)
100283025, 538810728, 1690090, 37628283, 119944992, 288941565, 13025172487, ss2225436708, ss3028659016, ss3650908594, ss3702681933, ss3821261800, ss3846848362, ss3981250282, ss5073395901, ss5307093913, ss5499639188, ss5612757090, ss5786107888, ss5817561918, ss5852272345, ss5927939497	NC_000019.10:33819894:A:G	NC_000019.10:33819894:A:G	(self)
ss10932071, ss21509431	NT_011109.15:6579017:A:G	NC_000019.10:33819894:A:G	(self)
ss29732, ss371889, ss630772, ss1249279, ss1307191, ss1966787, ss1974680, ss24525942, ss44196094, ss96302636, ss103435685, ss137653923, ss160605224	NT_011109.16:6579017:A:G	NC_000019.10:33819894: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 rs29939

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

rs29939