Name: rs2040107
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.

rs2040107

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr21:33303657 (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>A / C>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.216517 (57310/264690, TOPMED)
C=0.212675 (29794/140092, GnomAD)
C=0.20964 (5924/28258, 14KJPN) (+ 16 more)
C=0.25160 (4471/17770, ALFA)
C=0.20907 (3504/16760, 8.3KJPN)
C=0.1908 (1222/6404, 1000G_30x)
C=0.1937 (970/5008, 1000G)
C=0.2554 (1144/4480, Estonian)
C=0.2927 (1128/3854, ALSPAC)
C=0.2802 (1039/3708, TWINSUK)
C=0.2846 (834/2930, KOREAN)
C=0.1742 (310/1780, HapMap)
C=0.291 (290/998, GoNL)
C=0.283 (170/600, NorthernSweden)
C=0.165 (82/498, SGDP_PRJ)
C=0.301 (65/216, Qatari)
C=0.248 (53/214, Vietnamese)
C=0.27 (12/44, Siberian)
C=0.38 (15/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: None
Publications: 1 citation
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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	17770	C=0.25160	G=0.74840, T=0.00000	0.078334	0.575127	0.346539	30
European	Sub	13688	C=0.28784	G=0.71216, T=0.00000	0.091175	0.515488	0.393337	7
African	Sub	2428	C=0.0482	G=0.9518, T=0.0000	0.008237	0.911862	0.079901	11
African Others	Sub	90	C=0.00	G=1.00, T=0.00	0.0	1.0	0.0	N/A
African American	Sub	2338	C=0.0500	G=0.9500, T=0.0000	0.008554	0.908469	0.082977	11
Asian	Sub	112	C=0.188	G=0.812, T=0.000	0.053571	0.678571	0.267857	1
East Asian	Sub	86	C=0.22	G=0.78, T=0.00	0.069767	0.627907	0.302326	0
Other Asian	Sub	26	C=0.08	G=0.92, T=0.00	0.0	0.846154	0.153846	0
Latin American 1	Sub	146	C=0.219	G=0.781, T=0.000	0.068493	0.630137	0.30137	1
Latin American 2	Sub	610	C=0.323	G=0.677, T=0.000	0.108197	0.462295	0.429508	0
South Asian	Sub	98	C=0.21	G=0.79, T=0.00	0.040816	0.612245	0.346939	0
Other	Sub	688	C=0.208	G=0.792, T=0.000	0.055233	0.639535	0.305233	1

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=0.216517	G=0.783483
gnomAD - Genomes	Global	Study-wide	140092	C=0.212675	G=0.787325
gnomAD - Genomes	European	Sub	75858	C=0.27588	G=0.72412
gnomAD - Genomes	African	Sub	41994	C=0.05582	G=0.94418
gnomAD - Genomes	American	Sub	13644	C=0.29258	G=0.70742
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	C=0.3859	G=0.6141
gnomAD - Genomes	East Asian	Sub	3124	C=0.2558	G=0.7442
gnomAD - Genomes	Other	Sub	2150	C=0.2088	G=0.7912
14KJPN	JAPANESE	Study-wide	28258	C=0.20964	G=0.79036
Allele Frequency Aggregator	Total	Global	17770	C=0.25160	G=0.74840, T=0.00000
Allele Frequency Aggregator	European	Sub	13688	C=0.28784	G=0.71216, T=0.00000
Allele Frequency Aggregator	African	Sub	2428	C=0.0482	G=0.9518, T=0.0000
Allele Frequency Aggregator	Other	Sub	688	C=0.208	G=0.792, T=0.000
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.323	G=0.677, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.219	G=0.781, T=0.000
Allele Frequency Aggregator	Asian	Sub	112	C=0.188	G=0.812, T=0.000
Allele Frequency Aggregator	South Asian	Sub	98	C=0.21	G=0.79, T=0.00
8.3KJPN	JAPANESE	Study-wide	16760	C=0.20907	G=0.79093
1000Genomes_30x	Global	Study-wide	6404	C=0.1908	G=0.8092
1000Genomes_30x	African	Sub	1786	C=0.0101	G=0.9899
1000Genomes_30x	Europe	Sub	1266	C=0.3009	G=0.6991
1000Genomes_30x	South Asian	Sub	1202	C=0.1481	G=0.8519
1000Genomes_30x	East Asian	Sub	1170	C=0.2487	G=0.7513
1000Genomes_30x	American	Sub	980	C=0.361	G=0.639
1000Genomes	Global	Study-wide	5008	C=0.1937	G=0.8063
1000Genomes	African	Sub	1322	C=0.0159	G=0.9841
1000Genomes	East Asian	Sub	1008	C=0.2450	G=0.7550
1000Genomes	Europe	Sub	1006	C=0.3022	G=0.6978
1000Genomes	South Asian	Sub	978	C=0.153	G=0.847
1000Genomes	American	Sub	694	C=0.357	G=0.643
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.2554	G=0.7446
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.2927	G=0.7073
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.2802	G=0.7198
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.2846	A=0.0000, G=0.7154
HapMap	Global	Study-wide	1780	C=0.1742	G=0.8258
HapMap	American	Sub	768	C=0.237	G=0.763
HapMap	African	Sub	586	C=0.044	G=0.956
HapMap	Asian	Sub	250	C=0.228	G=0.772
HapMap	Europe	Sub	176	C=0.256	G=0.744
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.291	G=0.709
Northern Sweden	ACPOP	Study-wide	600	C=0.283	G=0.717
SGDP_PRJ	Global	Study-wide	498	C=0.165	G=0.835
Qatari	Global	Study-wide	216	C=0.301	G=0.699
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.248	G=0.752
Siberian	Global	Study-wide	44	C=0.27	G=0.73
The Danish reference pan genome	Danish	Study-wide	40	C=0.38	G=0.62

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 21	NC_000021.9:g.33303657C>A
GRCh38.p14 chr 21	NC_000021.9:g.33303657C>G
GRCh38.p14 chr 21	NC_000021.9:g.33303657C>T
GRCh37.p13 chr 21	NC_000021.8:g.34675962C>A
GRCh37.p13 chr 21	NC_000021.8:g.34675962C>G
GRCh37.p13 chr 21	NC_000021.8:g.34675962C>T

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=	A	G	T
GRCh38.p14 chr 21	NC_000021.9:g.33303657=	NC_000021.9:g.33303657C>A	NC_000021.9:g.33303657C>G	NC_000021.9:g.33303657C>T
GRCh37.p13 chr 21	NC_000021.8:g.34675962=	NC_000021.8:g.34675962C>A	NC_000021.8:g.34675962C>G	NC_000021.8:g.34675962C>T

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#.

79 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss2949630	Apr 12, 2001 (94)
2	PERLEGEN	ss4013234	Sep 28, 2001 (100)
3	SC_JCM	ss4026406	Sep 28, 2001 (100)
4	BCM_SSAHASNP	ss10985337	Jul 11, 2003 (116)
5	WI_SSAHASNP	ss12510610	Jul 11, 2003 (116)
6	CSHL-HAPMAP	ss17704148	Feb 27, 2004 (120)
7	PERLEGEN	ss24583870	Sep 20, 2004 (123)
8	ABI	ss44271159	Mar 14, 2006 (126)
9	AFFY	ss66218371	Nov 30, 2006 (127)
10	PERLEGEN	ss69252691	May 17, 2007 (127)
11	AFFY	ss76364820	Dec 06, 2007 (129)
12	KRIBB_YJKIM	ss81667009	Dec 16, 2007 (130)
13	BCMHGSC_JDW	ss91825994	Mar 24, 2008 (129)
14	BGI	ss106211379	Feb 03, 2009 (130)
15	1000GENOMES	ss112441930	Jan 25, 2009 (130)
16	1000GENOMES	ss113840558	Jan 25, 2009 (130)
17	ILLUMINA-UK	ss117511994	Dec 01, 2009 (131)
18	ENSEMBL	ss138310472	Dec 01, 2009 (131)
19	ENSEMBL	ss161358739	Dec 01, 2009 (131)
20	COMPLETE_GENOMICS	ss167943219	Jul 04, 2010 (132)
21	COMPLETE_GENOMICS	ss169375427	Jul 04, 2010 (132)
22	COMPLETE_GENOMICS	ss171983871	Jul 04, 2010 (132)
23	AFFY	ss173390091	Jul 04, 2010 (132)
24	BUSHMAN	ss204006235	Jul 04, 2010 (132)
25	1000GENOMES	ss237968377	Jul 15, 2010 (132)
26	1000GENOMES	ss244109922	Jul 15, 2010 (132)
27	GMI	ss283528856	May 04, 2012 (137)
28	PJP	ss292703916	May 09, 2011 (134)
29	TISHKOFF	ss566472844	Apr 25, 2013 (138)
30	SSMP	ss662383257	Apr 25, 2013 (138)
31	EVA-GONL	ss995082891	Aug 21, 2014 (142)
32	JMKIDD_LAB	ss1082473217	Aug 21, 2014 (142)
33	1000GENOMES	ss1366159360	Aug 21, 2014 (142)
34	DDI	ss1429174091	Apr 01, 2015 (144)
35	EVA_GENOME_DK	ss1579649309	Apr 01, 2015 (144)
36	EVA_UK10K_ALSPAC	ss1639489983	Apr 01, 2015 (144)
37	EVA_UK10K_TWINSUK	ss1682484016	Apr 01, 2015 (144)
38	EVA_DECODE	ss1699152599	Apr 01, 2015 (144)
39	EVA_SVP	ss1713720562	Apr 01, 2015 (144)
40	HAMMER_LAB	ss1809669946	Sep 08, 2015 (146)
41	WEILL_CORNELL_DGM	ss1938634127	Feb 12, 2016 (147)
42	GENOMED	ss1969217023	Jul 19, 2016 (147)
43	JJLAB	ss2030088457	Sep 14, 2016 (149)
44	USC_VALOUEV	ss2158692400	Dec 20, 2016 (150)
45	HUMAN_LONGEVITY	ss2245515590	Dec 20, 2016 (150)
46	SYSTEMSBIOZJU	ss2629542998	Nov 08, 2017 (151)
47	GRF	ss2704422180	Nov 08, 2017 (151)
48	GNOMAD	ss2971439630	Nov 08, 2017 (151)
49	SWEGEN	ss3018838448	Nov 08, 2017 (151)
50	BIOINF_KMB_FNS_UNIBA	ss3028882834	Nov 08, 2017 (151)
51	CSHL	ss3352703035	Nov 08, 2017 (151)
52	EGCUT_WGS	ss3685414583	Jul 13, 2019 (153)
53	EVA_DECODE	ss3707666828	Jul 13, 2019 (153)
54	ACPOP	ss3743702555	Jul 13, 2019 (153)
55	EVA	ss3759067403	Jul 13, 2019 (153)
56	PACBIO	ss3788752658	Jul 13, 2019 (153)
57	PACBIO	ss3793628232	Jul 13, 2019 (153)
58	PACBIO	ss3798514353	Jul 13, 2019 (153)
59	KHV_HUMAN_GENOMES	ss3822234804	Jul 13, 2019 (153)
60	EVA	ss3835857152	Apr 27, 2020 (154)
61	EVA	ss3841555495	Apr 27, 2020 (154)
62	EVA	ss3847069074	Apr 27, 2020 (154)
63	SGDP_PRJ	ss3889934263	Apr 27, 2020 (154)
64	KRGDB	ss3940288251	Apr 27, 2020 (154)
65	TOPMED	ss5100552328	Apr 27, 2021 (155)
66	TOMMO_GENOMICS	ss5231388228	Apr 27, 2021 (155)
67	1000G_HIGH_COVERAGE	ss5310108362	Oct 13, 2022 (156)
68	EVA	ss5439682321	Oct 13, 2022 (156)
69	HUGCELL_USP	ss5502165671	Oct 13, 2022 (156)
70	EVA	ss5512313732	Oct 13, 2022 (156)
71	1000G_HIGH_COVERAGE	ss5617200265	Oct 13, 2022 (156)
72	SANFORD_IMAGENETICS	ss5663949467	Oct 13, 2022 (156)
73	TOMMO_GENOMICS	ss5791862561	Oct 13, 2022 (156)
74	YY_MCH	ss5818417830	Oct 13, 2022 (156)
75	EVA	ss5838995372	Oct 13, 2022 (156)
76	EVA	ss5853290956	Oct 13, 2022 (156)
77	EVA	ss5892228707	Oct 13, 2022 (156)
78	EVA	ss5958841845	Oct 13, 2022 (156)
79	EVA	ss5981112119	Oct 13, 2022 (156)
80	1000Genomes	NC_000021.8 - 34675962	Oct 12, 2018 (152)
81	1000Genomes_30x	NC_000021.9 - 33303657	Oct 13, 2022 (156)
82	The Avon Longitudinal Study of Parents and Children	NC_000021.8 - 34675962	Oct 12, 2018 (152)
83	Genetic variation in the Estonian population	NC_000021.8 - 34675962	Oct 12, 2018 (152)
84	The Danish reference pan genome	NC_000021.8 - 34675962	Apr 27, 2020 (154)
85	gnomAD - Genomes	NC_000021.9 - 33303657	Apr 27, 2021 (155)
86	Genome of the Netherlands Release 5	NC_000021.8 - 34675962	Apr 27, 2020 (154)
87	HapMap	NC_000021.9 - 33303657	Apr 27, 2020 (154)
88	KOREAN population from KRGDB	NC_000021.8 - 34675962	Apr 27, 2020 (154)
89	Northern Sweden	NC_000021.8 - 34675962	Jul 13, 2019 (153)
90	Qatari	NC_000021.8 - 34675962	Apr 27, 2020 (154)
91	SGDP_PRJ	NC_000021.8 - 34675962	Apr 27, 2020 (154)
92	Siberian	NC_000021.8 - 34675962	Apr 27, 2020 (154)
93	8.3KJPN	NC_000021.8 - 34675962	Apr 27, 2021 (155)
94	14KJPN	NC_000021.9 - 33303657	Oct 13, 2022 (156)
95	TopMed	NC_000021.9 - 33303657	Apr 27, 2021 (155)
96	UK 10K study - Twins	NC_000021.8 - 34675962	Oct 12, 2018 (152)
97	A Vietnamese Genetic Variation Database	NC_000021.8 - 34675962	Jul 13, 2019 (153)
98	ALFA	NC_000021.9 - 33303657	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)
rs17710308	Oct 07, 2004 (123)
rs61575381	Feb 26, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
47465645, ss3940288251	NC_000021.8:34675961:C:A	NC_000021.9:33303656:C:A	(self)
ss66218371, ss76364820, ss91825994, ss112441930, ss113840558, ss117511994, ss167943219, ss169375427, ss171983871, ss173390091, ss204006235, ss283528856, ss292703916, ss1699152599, ss1713720562	NC_000021.7:33597831:C:G	NC_000021.9:33303656:C:G	(self)
79674105, 44089881, 31152831, 5814248, 19641763, 47465645, 16987420, 20676049, 41951243, 11208754, 89357535, 44089881, 9729486, ss237968377, ss244109922, ss566472844, ss662383257, ss995082891, ss1082473217, ss1366159360, ss1429174091, ss1579649309, ss1639489983, ss1682484016, ss1809669946, ss1938634127, ss1969217023, ss2030088457, ss2158692400, ss2629542998, ss2704422180, ss2971439630, ss3018838448, ss3352703035, ss3685414583, ss3743702555, ss3759067403, ss3788752658, ss3793628232, ss3798514353, ss3835857152, ss3841555495, ss3889934263, ss3940288251, ss5231388228, ss5439682321, ss5512313732, ss5663949467, ss5838995372, ss5958841845, ss5981112119	NC_000021.8:34675961:C:G	NC_000021.9:33303656:C:G	(self)
104726200, 562316784, 2202698, 125699665, 375661274, 4157638069, ss2245515590, ss3028882834, ss3707666828, ss3822234804, ss3847069074, ss5100552328, ss5310108362, ss5502165671, ss5617200265, ss5791862561, ss5818417830, ss5853290956, ss5892228707	NC_000021.9:33303656:C:G	NC_000021.9:33303656:C:G	(self)
ss10985337, ss12510610	NT_011512.8:20336356:C:G	NC_000021.9:33303656:C:G	(self)
ss17704148	NT_011512.9:20336357:C:G	NC_000021.9:33303656:C:G	(self)
ss2949630, ss4013234, ss4026406, ss24583870, ss44271159, ss69252691, ss81667009, ss106211379, ss138310472, ss161358739	NT_011512.11:20337832:C:G	NC_000021.9:33303656:C:G	(self)
4157638069	NC_000021.9:33303656:C:T	NC_000021.9:33303656:C:T	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs2040107

PMID	Title	Author	Year	Journal
21418175	Genetic variation in Th1/Th2 pathway genes and risk of non-Hodgkin lymphoma: a pooled analysis of three population-based case-control studies.	Lan Q et al.	2011	British journal of haematology

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

rs2040107