Name: rs439963
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.

rs439963

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr16:11270926 (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>C
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.026635 (7050/264690, TOPMED)
T=0.025920 (3635/140240, GnomAD)
T=0.00000 (0/28258, 14KJPN) (+ 15 more)
T=0.01297 (281/21658, ALFA)
T=0.00006 (1/16760, 8.3KJPN)
T=0.0247 (158/6404, 1000G_30x)
T=0.0234 (117/5008, 1000G)
T=0.0003 (1/3854, ALSPAC)
T=0.0003 (1/3708, TWINSUK)
T=0.0000 (0/2930, KOREAN)
T=0.0000 (0/1832, Korea1K)
T=0.0510 (69/1354, HapMap)
T=0.000 (0/600, NorthernSweden)
T=0.007 (4/558, SGDP_PRJ)
T=0.009 (2/216, Qatari)
T=0.000 (0/214, Vietnamese)
T=0.00 (0/56, Siberian)
T=0.00 (0/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: TNP2 : 2KB Upstream Variant
LOC105371082 : 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	21658	T=0.01297	C=0.98703
European	Sub	15668	T=0.00006	C=0.99994
African	Sub	3624	T=0.0709	C=0.9291
African Others	Sub	126	T=0.095	C=0.905
African American	Sub	3498	T=0.0700	C=0.9300
Asian	Sub	160	T=0.000	C=1.000
East Asian	Sub	102	T=0.000	C=1.000
Other Asian	Sub	58	T=0.00	C=1.00
Latin American 1	Sub	212	T=0.014	C=0.986
Latin American 2	Sub	754	T=0.003	C=0.997
South Asian	Sub	110	T=0.000	C=1.000
Other	Sub	1130	T=0.0159	C=0.9841

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	T=0.026635	C=0.973365
gnomAD - Genomes	Global	Study-wide	140240	T=0.025920	C=0.974080
gnomAD - Genomes	European	Sub	75956	T=0.00036	C=0.99964
gnomAD - Genomes	African	Sub	42014	T=0.08273	C=0.91727
gnomAD - Genomes	American	Sub	13660	T=0.00688	C=0.99312
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	T=0.0000	C=1.0000
gnomAD - Genomes	East Asian	Sub	3134	T=0.0000	C=1.0000
gnomAD - Genomes	Other	Sub	2152	T=0.0177	C=0.9823
14KJPN	JAPANESE	Study-wide	28258	T=0.00000	C=1.00000
Allele Frequency Aggregator	Total	Global	21658	T=0.01297	C=0.98703
Allele Frequency Aggregator	European	Sub	15668	T=0.00006	C=0.99994
Allele Frequency Aggregator	African	Sub	3624	T=0.0709	C=0.9291
Allele Frequency Aggregator	Other	Sub	1130	T=0.0159	C=0.9841
Allele Frequency Aggregator	Latin American 2	Sub	754	T=0.003	C=0.997
Allele Frequency Aggregator	Latin American 1	Sub	212	T=0.014	C=0.986
Allele Frequency Aggregator	Asian	Sub	160	T=0.000	C=1.000
Allele Frequency Aggregator	South Asian	Sub	110	T=0.000	C=1.000
8.3KJPN	JAPANESE	Study-wide	16760	T=0.00006	C=0.99994
1000Genomes_30x	Global	Study-wide	6404	T=0.0247	C=0.9753
1000Genomes_30x	African	Sub	1786	T=0.0868	C=0.9132
1000Genomes_30x	Europe	Sub	1266	T=0.0000	C=1.0000
1000Genomes_30x	South Asian	Sub	1202	T=0.0000	C=1.0000
1000Genomes_30x	East Asian	Sub	1170	T=0.0000	C=1.0000
1000Genomes_30x	American	Sub	980	T=0.003	C=0.997
1000Genomes	Global	Study-wide	5008	T=0.0234	C=0.9766
1000Genomes	African	Sub	1322	T=0.0862	C=0.9138
1000Genomes	East Asian	Sub	1008	T=0.0000	C=1.0000
1000Genomes	Europe	Sub	1006	T=0.0000	C=1.0000
1000Genomes	South Asian	Sub	978	T=0.000	C=1.000
1000Genomes	American	Sub	694	T=0.004	C=0.996
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.0003	C=0.9997
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.0003	C=0.9997
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.0000	C=1.0000
Korean Genome Project	KOREAN	Study-wide	1832	T=0.0000	C=1.0000
HapMap	Global	Study-wide	1354	T=0.0510	C=0.9490
HapMap	African	Sub	692	T=0.084	C=0.916
HapMap	American	Sub	494	T=0.020	C=0.980
HapMap	Asian	Sub	168	T=0.006	C=0.994
Northern Sweden	ACPOP	Study-wide	600	T=0.000	C=1.000
SGDP_PRJ	Global	Study-wide	558	T=0.007	C=0.993
Qatari	Global	Study-wide	216	T=0.009	C=0.991
A Vietnamese Genetic Variation Database	Global	Study-wide	214	T=0.000	C=1.000
Siberian	Global	Study-wide	56	T=0.00	C=1.00
The Danish reference pan genome	Danish	Study-wide	40	T=0.00	C=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 16	NC_000016.10:g.11270926T>C
GRCh37.p13 chr 16	NC_000016.9:g.11364783T>C

Gene: TNP2, transition protein 2 (minus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
TNP2 transcript	NM_005425.5:c.	N/A	Upstream Transcript Variant

Gene: LOC105371082, uncharacterized LOC105371082 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105371082 transcript variant X2	XR_933070.4:n.	N/A	Intron Variant
LOC105371082 transcript variant X1	XR_007064985.1:n.	N/A	Genic Upstream Transcript Variant
LOC105371082 transcript variant X6	XR_933071.3:n.	N/A	Genic Upstream Transcript Variant
LOC105371082 transcript variant X5	XR_933072.3:n.	N/A	Genic Upstream Transcript Variant
LOC105371082 transcript variant X3	XR_933073.3:n.	N/A	Genic Upstream Transcript Variant
LOC105371082 transcript variant X4	XR_933074.3:n.	N/A	Genic Upstream Transcript Variant
LOC105371082 transcript variant X7	XR_933075.3:n.	N/A	Genic Upstream 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	T=	C
GRCh38.p14 chr 16	NC_000016.10:g.11270926=	NC_000016.10:g.11270926T>C
GRCh37.p13 chr 16	NC_000016.9:g.11364783=	NC_000016.9:g.11364783T>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#.

82 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss586733	Jul 16, 2000 (80)
2	BCM_SSAHASNP	ss10841364	Jul 11, 2003 (116)
3	BCM_SSAHASNP	ss14254360	Dec 05, 2003 (119)
4	SSAHASNP	ss21300572	Apr 05, 2004 (121)
5	AFFY	ss66218891	Dec 02, 2006 (127)
6	AFFY	ss76365262	Dec 08, 2007 (130)
7	HGSV	ss77312919	Dec 06, 2007 (129)
8	HGSV	ss78822479	Dec 06, 2007 (129)
9	KRIBB_YJKIM	ss81421614	Dec 15, 2007 (130)
10	HGSV	ss82564272	Dec 14, 2007 (130)
11	BCMHGSC_JDW	ss90320920	Mar 24, 2008 (129)
12	HUMANGENOME_JCVI	ss96625944	Feb 03, 2009 (130)
13	BGI	ss106461916	Feb 03, 2009 (130)
14	1000GENOMES	ss109203287	Jan 23, 2009 (130)
15	1000GENOMES	ss114857037	Jan 25, 2009 (130)
16	ILLUMINA-UK	ss118195609	Dec 01, 2009 (131)
17	ENSEMBL	ss136594787	Dec 01, 2009 (131)
18	ENSEMBL	ss136798610	Dec 01, 2009 (131)
19	GMI	ss157106978	Dec 01, 2009 (131)
20	COMPLETE_GENOMICS	ss167864386	Jul 04, 2010 (132)
21	COMPLETE_GENOMICS	ss169188174	Jul 04, 2010 (132)
22	COMPLETE_GENOMICS	ss170981630	Jul 04, 2010 (132)
23	BUSHMAN	ss201455740	Jul 04, 2010 (132)
24	BCM-HGSC-SUB	ss207472402	Jul 04, 2010 (132)
25	1000GENOMES	ss227150500	Jul 14, 2010 (132)
26	1000GENOMES	ss236958444	Jul 15, 2010 (132)
27	1000GENOMES	ss243311599	Jul 15, 2010 (132)
28	BL	ss255518868	May 09, 2011 (134)
29	GMI	ss282441991	May 04, 2012 (137)
30	GMI	ss287036909	Apr 25, 2013 (138)
31	PJP	ss291921331	May 09, 2011 (134)
32	TISHKOFF	ss564790533	Apr 25, 2013 (138)
33	SSMP	ss660534658	Apr 25, 2013 (138)
34	JMKIDD_LAB	ss1080496521	Aug 21, 2014 (142)
35	1000GENOMES	ss1355434159	Aug 21, 2014 (142)
36	DDI	ss1427783159	Apr 01, 2015 (144)
37	EVA_GENOME_DK	ss1577841308	Apr 01, 2015 (144)
38	EVA_UK10K_ALSPAC	ss1634037517	Apr 01, 2015 (144)
39	EVA_UK10K_TWINSUK	ss1677031550	Apr 01, 2015 (144)
40	EVA_SVP	ss1713526910	Apr 01, 2015 (144)
41	HAMMER_LAB	ss1808428370	Sep 08, 2015 (146)
42	WEILL_CORNELL_DGM	ss1935711629	Feb 12, 2016 (147)
43	GENOMED	ss1968223839	Jul 19, 2016 (147)
44	JJLAB	ss2028642394	Sep 14, 2016 (149)
45	ILLUMINA	ss2094888558	Dec 20, 2016 (150)
46	ILLUMINA	ss2095064076	Dec 20, 2016 (150)
47	USC_VALOUEV	ss2157053629	Dec 20, 2016 (150)
48	HUMAN_LONGEVITY	ss2210724784	Dec 20, 2016 (150)
49	SYSTEMSBIOZJU	ss2628815558	Nov 08, 2017 (151)
50	GRF	ss2701549587	Nov 08, 2017 (151)
51	GNOMAD	ss2940442927	Nov 08, 2017 (151)
52	SWEGEN	ss3014085112	Nov 08, 2017 (151)
53	BIOINF_KMB_FNS_UNIBA	ss3028147223	Nov 08, 2017 (151)
54	CSHL	ss3351343647	Nov 08, 2017 (151)
55	URBANLAB	ss3650466416	Oct 12, 2018 (152)
56	ILLUMINA	ss3652091344	Oct 12, 2018 (152)
57	EVA_DECODE	ss3698864152	Jul 13, 2019 (153)
58	ACPOP	ss3741347000	Jul 13, 2019 (153)
59	EVA	ss3753702177	Jul 13, 2019 (153)
60	PACBIO	ss3787983924	Jul 13, 2019 (153)
61	PACBIO	ss3792976549	Jul 13, 2019 (153)
62	PACBIO	ss3797861514	Jul 13, 2019 (153)
63	KHV_HUMAN_GENOMES	ss3818998432	Jul 13, 2019 (153)
64	EVA	ss3834481942	Apr 27, 2020 (154)
65	EVA	ss3840846126	Apr 27, 2020 (154)
66	EVA	ss3846337373	Apr 27, 2020 (154)
67	SGDP_PRJ	ss3883968197	Apr 27, 2020 (154)
68	KRGDB	ss3933264485	Apr 27, 2020 (154)
69	KOGIC	ss3977135998	Apr 27, 2020 (154)
70	TOPMED	ss5008180939	Apr 27, 2021 (155)
71	TOMMO_GENOMICS	ss5218473423	Apr 27, 2021 (155)
72	1000G_HIGH_COVERAGE	ss5300176556	Oct 16, 2022 (156)
73	HUGCELL_USP	ss5493700092	Oct 16, 2022 (156)
74	1000G_HIGH_COVERAGE	ss5602425444	Oct 16, 2022 (156)
75	SANFORD_IMAGENETICS	ss5658489166	Oct 16, 2022 (156)
76	TOMMO_GENOMICS	ss5772967730	Oct 16, 2022 (156)
77	YY_MCH	ss5815768171	Oct 16, 2022 (156)
78	EVA	ss5846121200	Oct 16, 2022 (156)
79	EVA	ss5851496833	Oct 16, 2022 (156)
80	EVA	ss5898337173	Oct 16, 2022 (156)
81	EVA	ss5949921581	Oct 16, 2022 (156)
82	EVA	ss5980906164	Oct 16, 2022 (156)
83	1000Genomes	NC_000016.9 - 11364783	Oct 12, 2018 (152)
84	1000Genomes_30x	NC_000016.10 - 11270926	Oct 16, 2022 (156)
85	The Avon Longitudinal Study of Parents and Children	NC_000016.9 - 11364783	Oct 12, 2018 (152)
86	The Danish reference pan genome	NC_000016.9 - 11364783	Apr 27, 2020 (154)
87	gnomAD - Genomes	NC_000016.10 - 11270926	Apr 27, 2021 (155)
88	HapMap	NC_000016.10 - 11270926	Apr 27, 2020 (154)
89	KOREAN population from KRGDB	NC_000016.9 - 11364783	Apr 27, 2020 (154)
90	Korean Genome Project	NC_000016.10 - 11270926	Apr 27, 2020 (154)
91	Northern Sweden	NC_000016.9 - 11364783	Jul 13, 2019 (153)
92	Qatari	NC_000016.9 - 11364783	Apr 27, 2020 (154)
93	SGDP_PRJ	NC_000016.9 - 11364783	Apr 27, 2020 (154)
94	Siberian	NC_000016.9 - 11364783	Apr 27, 2020 (154)
95	8.3KJPN	NC_000016.9 - 11364783	Apr 27, 2021 (155)
96	14KJPN	NC_000016.10 - 11270926	Oct 16, 2022 (156)
97	TopMed	NC_000016.10 - 11270926	Apr 27, 2021 (155)
98	UK 10K study - Twins	NC_000016.9 - 11364783	Oct 12, 2018 (152)
99	A Vietnamese Genetic Variation Database	NC_000016.9 - 11364783	Jul 13, 2019 (153)
100	ALFA	NC_000016.10 - 11270926	Apr 27, 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)
rs56588974	May 23, 2008 (130)
rs56727475	May 23, 2008 (130)
rs59515823	Feb 26, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss66218891, ss76365262, ss77312919, ss78822479, ss82564272, ss90320920, ss109203287, ss114857037, ss118195609, ss167864386, ss169188174, ss170981630, ss201455740, ss207472402, ss255518868, ss282441991, ss287036909, ss291921331, ss1713526910, ss2094888558	NC_000016.8:11272283:T:C	NC_000016.10:11270925:T:C	(self)
68570617, 38074111, 4056739, 40441879, 14631865, 17753551, 35985177, 9569983, 76442730, 38074111, 8460518, ss227150500, ss236958444, ss243311599, ss564790533, ss660534658, ss1080496521, ss1355434159, ss1427783159, ss1577841308, ss1634037517, ss1677031550, ss1808428370, ss1935711629, ss1968223839, ss2028642394, ss2095064076, ss2157053629, ss2628815558, ss2701549587, ss2940442927, ss3014085112, ss3351343647, ss3652091344, ss3741347000, ss3753702177, ss3787983924, ss3792976549, ss3797861514, ss3834481942, ss3840846126, ss3883968197, ss3933264485, ss5218473423, ss5658489166, ss5846121200, ss5949921581, ss5980906164	NC_000016.9:11364782:T:C	NC_000016.10:11270925:T:C	(self)
89951379, 483167680, 1352452, 33513999, 106804834, 223726600, 6525123711, ss2210724784, ss3028147223, ss3650466416, ss3698864152, ss3818998432, ss3846337373, ss3977135998, ss5008180939, ss5300176556, ss5493700092, ss5602425444, ss5772967730, ss5815768171, ss5851496833, ss5898337173	NC_000016.10:11270925:T:C	NC_000016.10:11270925:T:C	(self)
ss10841364	NT_010393.13:2676994:T:C	NC_000016.10:11270925:T:C	(self)
ss14254360, ss21300572	NT_010393.14:2676994:T:C	NC_000016.10:11270925:T:C	(self)
ss586733, ss81421614, ss96625944, ss106461916, ss136594787, ss136798610, ss157106978	NT_010393.16:11304782:T:C	NC_000016.10:11270925:T:C	(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 rs439963

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

rs439963