Name: rs2271961
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.

rs2271961

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr3:49840680 (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>A / T>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.484246 (128175/264690, TOPMED)
C=0.483443 (67713/140064, GnomAD)
C=0.23855 (6741/28258, 14KJPN) (+ 19 more)
C=0.46671 (11551/24750, ALFA)
C=0.23765 (3983/16760, 8.3KJPN)
C=0.4243 (2717/6404, 1000G_30x)
C=0.4173 (2090/5008, 1000G)
C=0.4661 (2088/4480, Estonian)
T=0.4875 (1879/3854, ALSPAC)
C=0.4968 (1842/3708, TWINSUK)
C=0.2222 (651/2930, KOREAN)
C=0.4560 (861/1888, HapMap)
C=0.2265 (415/1832, Korea1K)
C=0.472 (471/998, GoNL)
C=0.359 (225/626, Chileans)
T=0.492 (295/600, NorthernSweden)
T=0.354 (126/356, SGDP_PRJ)
C=0.491 (106/216, Qatari)
C=0.181 (38/210, Vietnamese)
T=0.50 (20/40, GENOME_DK)
C=0.50 (20/40, GENOME_DK)
T=0.33 (12/36, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: TRAIP : 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	24750	T=0.53329	A=0.00000, C=0.46671
European	Sub	16888	T=0.51824	A=0.00000, C=0.48176
African	Sub	3188	T=0.4191	A=0.0000, C=0.5809
African Others	Sub	110	T=0.418	A=0.000, C=0.582
African American	Sub	3078	T=0.4191	A=0.0000, C=0.5809
Asian	Sub	160	T=0.800	A=0.000, C=0.200
East Asian	Sub	102	T=0.824	A=0.000, C=0.176
Other Asian	Sub	58	T=0.76	A=0.00, C=0.24
Latin American 1	Sub	292	T=0.527	A=0.000, C=0.473
Latin American 2	Sub	2770	T=0.7047	A=0.0000, C=0.2953
South Asian	Sub	110	T=0.645	A=0.000, C=0.355
Other	Sub	1342	T=0.6006	A=0.0000, C=0.3994

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=0.515754	C=0.484246
gnomAD - Genomes	Global	Study-wide	140064	T=0.516557	C=0.483443
gnomAD - Genomes	European	Sub	75876	T=0.53465	C=0.46535
gnomAD - Genomes	African	Sub	41952	T=0.41474	C=0.58526
gnomAD - Genomes	American	Sub	13650	T=0.63011	C=0.36989
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	T=0.6146	C=0.3854
gnomAD - Genomes	East Asian	Sub	3114	T=0.8407	C=0.1593
gnomAD - Genomes	Other	Sub	2148	T=0.5228	C=0.4772
14KJPN	JAPANESE	Study-wide	28258	T=0.76145	C=0.23855
Allele Frequency Aggregator	Total	Global	24750	T=0.53329	A=0.00000, C=0.46671
Allele Frequency Aggregator	European	Sub	16888	T=0.51824	A=0.00000, C=0.48176
Allele Frequency Aggregator	African	Sub	3188	T=0.4191	A=0.0000, C=0.5809
Allele Frequency Aggregator	Latin American 2	Sub	2770	T=0.7047	A=0.0000, C=0.2953
Allele Frequency Aggregator	Other	Sub	1342	T=0.6006	A=0.0000, C=0.3994
Allele Frequency Aggregator	Latin American 1	Sub	292	T=0.527	A=0.000, C=0.473
Allele Frequency Aggregator	Asian	Sub	160	T=0.800	A=0.000, C=0.200
Allele Frequency Aggregator	South Asian	Sub	110	T=0.645	A=0.000, C=0.355
8.3KJPN	JAPANESE	Study-wide	16760	T=0.76235	C=0.23765
1000Genomes_30x	Global	Study-wide	6404	T=0.5757	C=0.4243
1000Genomes_30x	African	Sub	1786	T=0.3695	C=0.6305
1000Genomes_30x	Europe	Sub	1266	T=0.5245	C=0.4755
1000Genomes_30x	South Asian	Sub	1202	T=0.6181	C=0.3819
1000Genomes_30x	East Asian	Sub	1170	T=0.8359	C=0.1641
1000Genomes_30x	American	Sub	980	T=0.655	C=0.345
1000Genomes	Global	Study-wide	5008	T=0.5827	C=0.4173
1000Genomes	African	Sub	1322	T=0.3737	C=0.6263
1000Genomes	East Asian	Sub	1008	T=0.8343	C=0.1657
1000Genomes	Europe	Sub	1006	T=0.5288	C=0.4712
1000Genomes	South Asian	Sub	978	T=0.618	C=0.382
1000Genomes	American	Sub	694	T=0.644	C=0.356
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.5339	C=0.4661
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.4875	C=0.5125
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.5032	C=0.4968
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.7778	C=0.2222
HapMap	Global	Study-wide	1888	T=0.5440	C=0.4560
HapMap	American	Sub	766	T=0.610	C=0.390
HapMap	African	Sub	692	T=0.389	C=0.611
HapMap	Asian	Sub	254	T=0.783	C=0.217
HapMap	Europe	Sub	176	T=0.523	C=0.477
Korean Genome Project	KOREAN	Study-wide	1832	T=0.7735	C=0.2265
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.528	C=0.472
Chileans	Chilean	Study-wide	626	T=0.641	C=0.359
Northern Sweden	ACPOP	Study-wide	600	T=0.492	C=0.508
SGDP_PRJ	Global	Study-wide	356	T=0.354	C=0.646
Qatari	Global	Study-wide	216	T=0.509	C=0.491
A Vietnamese Genetic Variation Database	Global	Study-wide	210	T=0.819	C=0.181
The Danish reference pan genome	Danish	Study-wide	40	T=0.50	C=0.50
Siberian	Global	Study-wide	36	T=0.33	C=0.67

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 3	NC_000003.12:g.49840680T>A
GRCh38.p14 chr 3	NC_000003.12:g.49840680T>C
GRCh37.p13 chr 3	NC_000003.11:g.49878113T>A
GRCh37.p13 chr 3	NC_000003.11:g.49878113T>C
TRAIP RefSeqGene	NG_046695.1:g.20880A>T
TRAIP RefSeqGene	NG_046695.1:g.20880A>G

Gene: TRAIP, TRAF interacting protein (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TRAIP transcript	NM_005879.3:c.705+305A>T	N/A	Intron Variant
TRAIP transcript variant X1	XM_017005526.2:c.409-307A… XM_017005526.2:c.409-307A>T	N/A	Intron Variant
TRAIP transcript variant X3	XM_047447240.1:c.178-307A… XM_047447240.1:c.178-307A>T	N/A	Intron Variant
TRAIP transcript variant X2	XR_007094382.1: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	T=	A	C
GRCh38.p14 chr 3	NC_000003.12:g.49840680=	NC_000003.12:g.49840680T>A	NC_000003.12:g.49840680T>C
GRCh37.p13 chr 3	NC_000003.11:g.49878113=	NC_000003.11:g.49878113T>A	NC_000003.11:g.49878113T>C
TRAIP RefSeqGene	NG_046695.1:g.20880=	NG_046695.1:g.20880A>T	NG_046695.1:g.20880A>G
TRAIP transcript	NM_005879.2:c.705+305=	NM_005879.2:c.705+305A>T	NM_005879.2:c.705+305A>G
TRAIP transcript	NM_005879.3:c.705+305=	NM_005879.3:c.705+305A>T	NM_005879.3:c.705+305A>G
TRAIP transcript variant X1	XM_017005526.2:c.409-307=	XM_017005526.2:c.409-307A>T	XM_017005526.2:c.409-307A>G
TRAIP transcript variant X3	XM_047447240.1:c.178-307=	XM_047447240.1:c.178-307A>T	XM_047447240.1:c.178-307A>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#.

85 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	YUSUKE	ss3206908	Sep 28, 2001 (100)
2	WI_SSAHASNP	ss11552068	Jul 11, 2003 (116)
3	CSHL-HAPMAP	ss20185684	Feb 27, 2004 (120)
4	PERLEGEN	ss24669702	Sep 20, 2004 (123)
5	ABI	ss44372684	Mar 14, 2006 (126)
6	AFFY	ss66241493	Nov 30, 2006 (127)
7	AFFY	ss76387158	Dec 07, 2007 (129)
8	HGSV	ss77389198	Dec 07, 2007 (129)
9	KRIBB_YJKIM	ss81745460	Dec 15, 2007 (130)
10	BCMHGSC_JDW	ss92083128	Mar 24, 2008 (129)
11	HUMANGENOME_JCVI	ss96008326	Feb 06, 2009 (130)
12	1000GENOMES	ss110128493	Jan 24, 2009 (130)
13	ILLUMINA-UK	ss117077222	Feb 14, 2009 (130)
14	ENSEMBL	ss133213391	Dec 01, 2009 (131)
15	ENSEMBL	ss138854334	Dec 01, 2009 (131)
16	GMI	ss155438788	Dec 01, 2009 (131)
17	COMPLETE_GENOMICS	ss162114386	Jul 04, 2010 (132)
18	COMPLETE_GENOMICS	ss163395837	Jul 04, 2010 (132)
19	AFFY	ss173445904	Jul 04, 2010 (132)
20	BUSHMAN	ss202495413	Jul 04, 2010 (132)
21	BCM-HGSC-SUB	ss206156203	Jul 04, 2010 (132)
22	1000GENOMES	ss220127061	Jul 14, 2010 (132)
23	1000GENOMES	ss231813554	Jul 14, 2010 (132)
24	1000GENOMES	ss239228589	Jul 15, 2010 (132)
25	GMI	ss277117999	May 04, 2012 (137)
26	GMI	ss284642197	Apr 25, 2013 (138)
27	PJP	ss292792271	May 09, 2011 (134)
28	TISHKOFF	ss556600874	Apr 25, 2013 (138)
29	SSMP	ss650277834	Apr 25, 2013 (138)
30	EVA-GONL	ss978566684	Aug 21, 2014 (142)
31	JMKIDD_LAB	ss1070392140	Aug 21, 2014 (142)
32	1000GENOMES	ss1303907329	Aug 21, 2014 (142)
33	DDI	ss1429413551	Apr 01, 2015 (144)
34	EVA_GENOME_DK	ss1579954662	Apr 01, 2015 (144)
35	EVA_DECODE	ss1588037296	Apr 01, 2015 (144)
36	EVA_UK10K_ALSPAC	ss1607017488	Apr 01, 2015 (144)
37	EVA_UK10K_TWINSUK	ss1650011521	Apr 01, 2015 (144)
38	EVA_SVP	ss1712573885	Apr 01, 2015 (144)
39	HAMMER_LAB	ss1799251981	Sep 08, 2015 (146)
40	WEILL_CORNELL_DGM	ss1921809143	Feb 12, 2016 (147)
41	GENOMED	ss1969387438	Jul 19, 2016 (147)
42	JJLAB	ss2021464189	Sep 14, 2016 (149)
43	ILLUMINA	ss2094929193	Dec 20, 2016 (150)
44	ILLUMINA	ss2095131476	Dec 20, 2016 (150)
45	USC_VALOUEV	ss2149535998	Dec 20, 2016 (150)
46	HUMAN_LONGEVITY	ss2251369617	Dec 20, 2016 (150)
47	SYSTEMSBIOZJU	ss2625230180	Nov 08, 2017 (151)
48	GRF	ss2704908646	Nov 08, 2017 (151)
49	GNOMAD	ss2792684854	Nov 08, 2017 (151)
50	AFFY	ss2985256507	Nov 08, 2017 (151)
51	SWEGEN	ss2992276711	Nov 08, 2017 (151)
52	BIOINF_KMB_FNS_UNIBA	ss3024494135	Nov 08, 2017 (151)
53	CSHL	ss3345009102	Nov 08, 2017 (151)
54	URBANLAB	ss3647398677	Oct 12, 2018 (152)
55	ILLUMINA	ss3652711083	Oct 12, 2018 (152)
56	EGCUT_WGS	ss3660196951	Jul 13, 2019 (153)
57	EVA_DECODE	ss3709185479	Jul 13, 2019 (153)
58	ACPOP	ss3729867412	Jul 13, 2019 (153)
59	EVA	ss3760003086	Jul 13, 2019 (153)
60	PACBIO	ss3784307817	Jul 13, 2019 (153)
61	PACBIO	ss3789824785	Jul 13, 2019 (153)
62	PACBIO	ss3794698728	Jul 13, 2019 (153)
63	KHV_HUMAN_GENOMES	ss3803143450	Jul 13, 2019 (153)
64	EVA	ss3827798909	Apr 25, 2020 (154)
65	EVA	ss3837321455	Apr 25, 2020 (154)
66	EVA	ss3842746747	Apr 25, 2020 (154)
67	SGDP_PRJ	ss3855798391	Apr 25, 2020 (154)
68	KRGDB	ss3901642543	Apr 25, 2020 (154)
69	KOGIC	ss3951213656	Apr 25, 2020 (154)
70	TOPMED	ss4563832383	Apr 27, 2021 (155)
71	TOMMO_GENOMICS	ss5159049524	Apr 27, 2021 (155)
72	1000G_HIGH_COVERAGE	ss5254005320	Oct 12, 2022 (156)
73	EVA	ss5339656020	Oct 12, 2022 (156)
74	HUGCELL_USP	ss5453404409	Oct 12, 2022 (156)
75	EVA	ss5506985798	Oct 12, 2022 (156)
76	1000G_HIGH_COVERAGE	ss5532328834	Oct 12, 2022 (156)
77	SANFORD_IMAGENETICS	ss5624517730	Oct 12, 2022 (156)
78	SANFORD_IMAGENETICS	ss5632086754	Oct 12, 2022 (156)
79	TOMMO_GENOMICS	ss5690678878	Oct 12, 2022 (156)
80	YY_MCH	ss5803718810	Oct 12, 2022 (156)
81	EVA	ss5825723683	Oct 12, 2022 (156)
82	EVA	ss5853603423	Oct 12, 2022 (156)
83	EVA	ss5868738972	Oct 12, 2022 (156)
84	EVA	ss5960377089	Oct 12, 2022 (156)
85	EVA	ss5980145078	Oct 12, 2022 (156)
86	1000Genomes	NC_000003.11 - 49878113	Oct 12, 2018 (152)
87	1000Genomes_30x	NC_000003.12 - 49840680	Oct 12, 2022 (156)
88	The Avon Longitudinal Study of Parents and Children	NC_000003.11 - 49878113	Oct 12, 2018 (152)
89	Chileans	NC_000003.11 - 49878113	Apr 25, 2020 (154)
90	Genetic variation in the Estonian population	NC_000003.11 - 49878113	Oct 12, 2018 (152)
91	The Danish reference pan genome	NC_000003.11 - 49878113	Apr 25, 2020 (154)
92	gnomAD - Genomes	NC_000003.12 - 49840680	Apr 27, 2021 (155)
93	Genome of the Netherlands Release 5	NC_000003.11 - 49878113	Apr 25, 2020 (154)
94	HapMap	NC_000003.12 - 49840680	Apr 25, 2020 (154)
95	KOREAN population from KRGDB	NC_000003.11 - 49878113	Apr 25, 2020 (154)
96	Korean Genome Project	NC_000003.12 - 49840680	Apr 25, 2020 (154)
97	Northern Sweden	NC_000003.11 - 49878113	Jul 13, 2019 (153)
98	Qatari	NC_000003.11 - 49878113	Apr 25, 2020 (154)
99	SGDP_PRJ	NC_000003.11 - 49878113	Apr 25, 2020 (154)
100	Siberian	NC_000003.11 - 49878113	Apr 25, 2020 (154)
101	8.3KJPN	NC_000003.11 - 49878113	Apr 27, 2021 (155)
102	14KJPN	NC_000003.12 - 49840680	Oct 12, 2022 (156)
103	TopMed	NC_000003.12 - 49840680	Apr 27, 2021 (155)
104	UK 10K study - Twins	NC_000003.11 - 49878113	Oct 12, 2018 (152)
105	A Vietnamese Genetic Variation Database	NC_000003.11 - 49878113	Jul 13, 2019 (153)
106	ALFA	NC_000003.12 - 49840680	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)
rs17546252	Oct 07, 2004 (123)
rs58394399	Feb 27, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
3834561338	NC_000003.12:49840679:T:A	NC_000003.12:49840679:T:A	(self)
ss77389198	NC_000003.9:49853116:T:C	NC_000003.12:49840679:T:C	(self)
ss66241493, ss76387158, ss92083128, ss110128493, ss117077222, ss162114386, ss163395837, ss173445904, ss202495413, ss206156203, ss277117999, ss284642197, ss292792271, ss1588037296, ss1712573885, ss2094929193	NC_000003.10:49853116:T:C	NC_000003.12:49840679:T:C	(self)
15092204, 8392635, 283970, 5935199, 6119601, 3682155, 8819937, 3152277, 3851073, 7815371, 2052352, 17018831, 8392635, 1824493, ss220127061, ss231813554, ss239228589, ss556600874, ss650277834, ss978566684, ss1070392140, ss1303907329, ss1429413551, ss1579954662, ss1607017488, ss1650011521, ss1799251981, ss1921809143, ss1969387438, ss2021464189, ss2095131476, ss2149535998, ss2625230180, ss2704908646, ss2792684854, ss2985256507, ss2992276711, ss3345009102, ss3652711083, ss3660196951, ss3729867412, ss3760003086, ss3784307817, ss3789824785, ss3794698728, ss3827798909, ss3837321455, ss3855798391, ss3901642543, ss5159049524, ss5339656020, ss5506985798, ss5624517730, ss5632086754, ss5825723683, ss5960377089, ss5980145078	NC_000003.11:49878112:T:C	NC_000003.12:49840679:T:C	(self)
19854769, 107098160, 2355539, 7591657, 24515982, 401209938, 3834561338, ss2251369617, ss3024494135, ss3647398677, ss3709185479, ss3803143450, ss3842746747, ss3951213656, ss4563832383, ss5254005320, ss5453404409, ss5532328834, ss5690678878, ss5803718810, ss5853603423, ss5868738972	NC_000003.12:49840679:T:C	NC_000003.12:49840679:T:C	(self)
ss11552068	NT_006014.14:993185:T:C	NC_000003.12:49840679:T:C	(self)
ss20185684	NT_022517.16:49802124:T:C	NC_000003.12:49840679:T:C	(self)
ss3206908, ss24669702, ss44372684, ss81745460, ss96008326, ss133213391, ss138854334, ss155438788	NT_022517.18:49818112:T:C	NC_000003.12:49840679: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 rs2271961

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

rs2271961