Name: rs2851275
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.

rs2851275

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:99103732 (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 / A>T
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.313344 (82939/264690, TOPMED)
G=0.423472 (86844/205076, GENOGRAPHIC)
G=0.11498 (3249/28258, 14KJPN) (+ 19 more)
G=0.31596 (8886/28124, ALFA)
G=0.11611 (1946/16760, 8.3KJPN)
G=0.2851 (1826/6404, 1000G_30x)
G=0.2859 (1432/5008, 1000G)
G=0.4618 (2069/4480, Estonian)
G=0.4408 (1699/3854, ALSPAC)
G=0.4385 (1626/3708, TWINSUK)
G=0.1150 (336/2922, KOREAN)
G=0.2394 (453/1892, HapMap)
G=0.1075 (197/1832, Korea1K)
G=0.453 (452/998, GoNL)
G=0.283 (177/626, Chileans)
G=0.400 (240/600, NorthernSweden)
A=0.353 (103/292, SGDP_PRJ)
G=0.310 (67/216, Qatari)
G=0.126 (27/214, Vietnamese)
G=0.42 (22/52, Ancient Sardinia)
G=0.40 (16/40, GENOME_DK)
A=0.44 (14/32, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC100507053 : Intron Variant
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	28218	A=0.68364	G=0.31636, T=0.00000	0.502871	0.135587	0.361542	32
European	Sub	18382	A=0.60712	G=0.39288, T=0.00000	0.393211	0.178979	0.42781	32
African	Sub	5542	A=0.9177	G=0.0823, T=0.0000	0.848791	0.013353	0.137856	12
African Others	Sub	190	A=0.937	G=0.063, T=0.000	0.894737	0.021053	0.084211	5
African American	Sub	5352	A=0.9170	G=0.0830, T=0.0000	0.84716	0.013079	0.139761	10
Asian	Sub	136	A=0.868	G=0.132, T=0.000	0.779412	0.044118	0.176471	2
East Asian	Sub	82	A=0.95	G=0.05, T=0.00	0.902439	0.0	0.097561	0
Other Asian	Sub	54	A=0.74	G=0.26, T=0.00	0.592593	0.111111	0.296296	1
Latin American 1	Sub	226	A=0.752	G=0.248, T=0.000	0.59292	0.088496	0.318584	2
Latin American 2	Sub	2452	A=0.7080	G=0.2920, T=0.0000	0.517129	0.101142	0.381729	4
South Asian	Sub	38	A=0.68	G=0.32, T=0.00	0.578947	0.210526	0.210526	3
Other	Sub	1442	A=0.6900	G=0.3100, T=0.0000	0.504854	0.124827	0.370319	8

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=0.686656	G=0.313344
Genographic Project	Global	Study-wide	205076	A=0.576528	G=0.423472, T=0.000000
14KJPN	JAPANESE	Study-wide	28258	A=0.88502	G=0.11498
Allele Frequency Aggregator	Total	Global	28124	A=0.68404	G=0.31596, T=0.00000
Allele Frequency Aggregator	European	Sub	18306	A=0.60745	G=0.39255, T=0.00000
Allele Frequency Aggregator	African	Sub	5542	A=0.9177	G=0.0823, T=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	2452	A=0.7080	G=0.2920, T=0.0000
Allele Frequency Aggregator	Other	Sub	1424	A=0.6896	G=0.3104, T=0.0000
Allele Frequency Aggregator	Latin American 1	Sub	226	A=0.752	G=0.248, T=0.000
Allele Frequency Aggregator	Asian	Sub	136	A=0.868	G=0.132, T=0.000
Allele Frequency Aggregator	South Asian	Sub	38	A=0.68	G=0.32, T=0.00
8.3KJPN	JAPANESE	Study-wide	16760	A=0.88389	G=0.11611
1000Genomes_30x	Global	Study-wide	6404	A=0.7149	G=0.2851
1000Genomes_30x	African	Sub	1786	A=0.9110	G=0.0890
1000Genomes_30x	Europe	Sub	1266	A=0.5537	G=0.4463
1000Genomes_30x	South Asian	Sub	1202	A=0.4651	G=0.5349
1000Genomes_30x	East Asian	Sub	1170	A=0.8744	G=0.1256
1000Genomes_30x	American	Sub	980	A=0.682	G=0.318
1000Genomes	Global	Study-wide	5008	A=0.7141	G=0.2859
1000Genomes	African	Sub	1322	A=0.9107	G=0.0893
1000Genomes	East Asian	Sub	1008	A=0.8730	G=0.1270
1000Genomes	Europe	Sub	1006	A=0.5537	G=0.4463
1000Genomes	South Asian	Sub	978	A=0.468	G=0.532
1000Genomes	American	Sub	694	A=0.687	G=0.313
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.5382	G=0.4618
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.5592	G=0.4408
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.5615	G=0.4385
KOREAN population from KRGDB	KOREAN	Study-wide	2922	A=0.8850	G=0.1150
HapMap	Global	Study-wide	1892	A=0.7606	G=0.2394
HapMap	American	Sub	770	A=0.632	G=0.368
HapMap	African	Sub	692	A=0.902	G=0.098
HapMap	Asian	Sub	254	A=0.866	G=0.134
HapMap	Europe	Sub	176	A=0.614	G=0.386
Korean Genome Project	KOREAN	Study-wide	1832	A=0.8925	G=0.1075
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.547	G=0.453
Chileans	Chilean	Study-wide	626	A=0.717	G=0.283
Northern Sweden	ACPOP	Study-wide	600	A=0.600	G=0.400
SGDP_PRJ	Global	Study-wide	292	A=0.353	G=0.647
Qatari	Global	Study-wide	216	A=0.690	G=0.310
A Vietnamese Genetic Variation Database	Global	Study-wide	214	A=0.874	G=0.126
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	52	A=0.58	G=0.42
The Danish reference pan genome	Danish	Study-wide	40	A=0.60	G=0.40
Siberian	Global	Study-wide	32	A=0.44	G=0.56

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 4	NC_000004.12:g.99103732A>G
GRCh38.p14 chr 4	NC_000004.12:g.99103732A>T
GRCh37.p13 chr 4	NC_000004.11:g.100024883A>G
GRCh37.p13 chr 4	NC_000004.11:g.100024883A>T

Gene: LOC100507053, uncharacterized LOC100507053 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC100507053 transcript	NR_037884.1: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	A=	G	T
GRCh38.p14 chr 4	NC_000004.12:g.99103732=	NC_000004.12:g.99103732A>G	NC_000004.12:g.99103732A>T
GRCh37.p13 chr 4	NC_000004.11:g.100024883=	NC_000004.11:g.100024883A>G	NC_000004.11:g.100024883A>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#.

76 SubSNP, 24 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss4037154	Sep 28, 2001 (100)
2	BCM_SSAHASNP	ss14246793	Dec 05, 2003 (119)
3	WI_SSAHASNP	ss14606597	Dec 05, 2003 (119)
4	PERLEGEN	ss24275294	Sep 20, 2004 (123)
5	ABI	ss42140463	Mar 13, 2006 (126)
6	AFFY	ss66219899	Dec 01, 2006 (127)
7	AFFY	ss76366292	Dec 08, 2007 (130)
8	KRIBB_YJKIM	ss81892438	Dec 15, 2007 (130)
9	BCMHGSC_JDW	ss92702677	Mar 24, 2008 (129)
10	HUMANGENOME_JCVI	ss98986597	Feb 06, 2009 (130)
11	1000GENOMES	ss108169630	Jan 23, 2009 (130)
12	ENSEMBL	ss139537326	Dec 01, 2009 (131)
13	ENSEMBL	ss139781314	Dec 01, 2009 (131)
14	COMPLETE_GENOMICS	ss166942463	Jul 04, 2010 (132)
15	AFFY	ss173393891	Jul 04, 2010 (132)
16	BCM-HGSC-SUB	ss206300807	Jul 04, 2010 (132)
17	1000GENOMES	ss221098258	Jul 14, 2010 (132)
18	1000GENOMES	ss232514620	Jul 14, 2010 (132)
19	1000GENOMES	ss239779905	Jul 15, 2010 (132)
20	BL	ss253370391	May 09, 2011 (134)
21	GMI	ss277843933	May 04, 2012 (137)
22	PJP	ss293147175	May 09, 2011 (134)
23	TISHKOFF	ss557720447	Apr 25, 2013 (138)
24	SSMP	ss651525042	Apr 25, 2013 (138)
25	EVA-GONL	ss980448938	Aug 21, 2014 (142)
26	JMKIDD_LAB	ss1071786349	Aug 21, 2014 (142)
27	1000GENOMES	ss1310976335	Aug 21, 2014 (142)
28	DDI	ss1429982212	Apr 01, 2015 (144)
29	EVA_GENOME_DK	ss1580686844	Apr 01, 2015 (144)
30	EVA_DECODE	ss1589952963	Apr 01, 2015 (144)
31	EVA_UK10K_ALSPAC	ss1610734258	Apr 01, 2015 (144)
32	EVA_UK10K_TWINSUK	ss1653728291	Apr 01, 2015 (144)
33	EVA_SVP	ss1712692993	Apr 01, 2015 (144)
34	HAMMER_LAB	ss1801907280	Sep 08, 2015 (146)
35	WEILL_CORNELL_DGM	ss1923689113	Feb 12, 2016 (147)
36	GENOMED	ss1969816510	Jul 19, 2016 (147)
37	JJLAB	ss2022430391	Sep 14, 2016 (149)
38	USC_VALOUEV	ss2150559517	Dec 20, 2016 (150)
39	HUMAN_LONGEVITY	ss2265417932	Dec 20, 2016 (150)
40	SYSTEMSBIOZJU	ss2625714171	Nov 08, 2017 (151)
41	GRF	ss2706036577	Nov 08, 2017 (151)
42	GNOMAD	ss2812843966	Nov 08, 2017 (151)
43	AFFY	ss2985298801	Nov 08, 2017 (151)
44	AFFY	ss2985926485	Nov 08, 2017 (151)
45	SWEGEN	ss2995208729	Nov 08, 2017 (151)
46	BIOINF_KMB_FNS_UNIBA	ss3024990372	Nov 08, 2017 (151)
47	CSHL	ss3345861137	Nov 08, 2017 (151)
48	URBANLAB	ss3647802152	Oct 12, 2018 (152)
49	ILLUMINA	ss3654070668	Oct 12, 2018 (152)
50	EGCUT_WGS	ss3663104519	Jul 13, 2019 (153)
51	EVA_DECODE	ss3712654834	Jul 13, 2019 (153)
52	ACPOP	ss3731420775	Jul 13, 2019 (153)
53	EVA	ss3762166064	Jul 13, 2019 (153)
54	KHV_HUMAN_GENOMES	ss3805314341	Jul 13, 2019 (153)
55	EVA	ss3828702824	Apr 26, 2020 (154)
56	EVA	ss3837792332	Apr 26, 2020 (154)
57	EVA	ss3843230700	Apr 26, 2020 (154)
58	SGDP_PRJ	ss3859608646	Apr 26, 2020 (154)
59	KRGDB	ss3905886012	Apr 26, 2020 (154)
60	KOGIC	ss3954740739	Apr 26, 2020 (154)
61	EVA	ss3985085298	Apr 26, 2021 (155)
62	TOPMED	ss4624607451	Apr 26, 2021 (155)
63	TOMMO_GENOMICS	ss5167074543	Apr 26, 2021 (155)
64	1000G_HIGH_COVERAGE	ss5260285608	Oct 13, 2022 (156)
65	GENOGRAPHIC	ss5314500090	Oct 13, 2022 (156)
66	EVA	ss5350971128	Oct 13, 2022 (156)
67	HUGCELL_USP	ss5458928389	Oct 13, 2022 (156)
68	EVA	ss5507640831	Oct 13, 2022 (156)
69	1000G_HIGH_COVERAGE	ss5541951783	Oct 13, 2022 (156)
70	SANFORD_IMAGENETICS	ss5635663811	Oct 13, 2022 (156)
71	TOMMO_GENOMICS	ss5701804607	Oct 13, 2022 (156)
72	YY_MCH	ss5805353292	Oct 13, 2022 (156)
73	EVA	ss5844422746	Oct 13, 2022 (156)
74	EVA	ss5854355561	Oct 13, 2022 (156)
75	EVA	ss5864673657	Oct 13, 2022 (156)
76	EVA	ss5964054436	Oct 13, 2022 (156)
77	1000Genomes	NC_000004.11 - 100024883	Oct 12, 2018 (152)
78	1000Genomes_30x	NC_000004.12 - 99103732	Oct 13, 2022 (156)
79	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 100024883	Oct 12, 2018 (152)
80	Chileans	NC_000004.11 - 100024883	Apr 26, 2020 (154)
81	Genetic variation in the Estonian population	NC_000004.11 - 100024883	Oct 12, 2018 (152)
82	Genographic Project	NC_000004.12 - 99103732	Oct 13, 2022 (156)
83	The Danish reference pan genome	NC_000004.11 - 100024883	Apr 26, 2020 (154)
84	gnomAD - Genomes Submission ignored due to conflicting rows: Row 158806537 (NC_000004.12:99103731:A:G 46457/140042) Row 158806538 (NC_000004.12:99103731:A:T 3/140092)	-	Apr 26, 2021 (155)
85	gnomAD - Genomes Submission ignored due to conflicting rows: Row 158806537 (NC_000004.12:99103731:A:G 46457/140042) Row 158806538 (NC_000004.12:99103731:A:T 3/140092)	-	Apr 26, 2021 (155)
86	Genome of the Netherlands Release 5	NC_000004.11 - 100024883	Apr 26, 2020 (154)
87	HapMap	NC_000004.12 - 99103732	Apr 26, 2020 (154)
88	KOREAN population from KRGDB	NC_000004.11 - 100024883	Apr 26, 2020 (154)
89	Korean Genome Project	NC_000004.12 - 99103732	Apr 26, 2020 (154)
90	Northern Sweden	NC_000004.11 - 100024883	Jul 13, 2019 (153)
91	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000004.11 - 100024883	Apr 26, 2021 (155)
92	Qatari	NC_000004.11 - 100024883	Apr 26, 2020 (154)
93	SGDP_PRJ	NC_000004.11 - 100024883	Apr 26, 2020 (154)
94	Siberian	NC_000004.11 - 100024883	Apr 26, 2020 (154)
95	8.3KJPN	NC_000004.11 - 100024883	Apr 26, 2021 (155)
96	14KJPN	NC_000004.12 - 99103732	Oct 13, 2022 (156)
97	TopMed	NC_000004.12 - 99103732	Apr 26, 2021 (155)
98	UK 10K study - Twins	NC_000004.11 - 100024883	Oct 12, 2018 (152)
99	A Vietnamese Genetic Variation Database	NC_000004.11 - 100024883	Jul 13, 2019 (153)
100	ALFA	NC_000004.12 - 99103732	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)
rs17596004	Oct 07, 2004 (123)
rs56553997	May 26, 2008 (130)
rs60202681	Feb 27, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss66219899, ss76366292, ss92702677, ss108169630, ss166942463, ss173393891, ss206300807, ss253370391, ss277843933, ss293147175, ss1589952963, ss1712692993	NC_000004.10:100243905:A:G	NC_000004.12:99103731:A:G	(self)
22418379, 12470218, 322695, 8842767, 6851783, 5512436, 13063406, 4705640, 311225, 5731043, 11625626, 3075871, 25043850, 12470218, 2743955, ss221098258, ss232514620, ss239779905, ss557720447, ss651525042, ss980448938, ss1071786349, ss1310976335, ss1429982212, ss1580686844, ss1610734258, ss1653728291, ss1801907280, ss1923689113, ss1969816510, ss2022430391, ss2150559517, ss2625714171, ss2706036577, ss2812843966, ss2985298801, ss2985926485, ss2995208729, ss3345861137, ss3654070668, ss3663104519, ss3731420775, ss3762166064, ss3828702824, ss3837792332, ss3859608646, ss3905886012, ss3985085298, ss5167074543, ss5350971128, ss5507640831, ss5635663811, ss5844422746, ss5964054436	NC_000004.11:100024882:A:G	NC_000004.12:99103731:A:G	(self)
29477718, 67794, 2670064, 11118740, 35641711, 461985007, 9977758346, ss2265417932, ss3024990372, ss3647802152, ss3712654834, ss3805314341, ss3843230700, ss3954740739, ss4624607451, ss5260285608, ss5314500090, ss5458928389, ss5541951783, ss5701804607, ss5805353292, ss5854355561, ss5864673657	NC_000004.12:99103731:A:G	NC_000004.12:99103731:A:G	(self)
ss14246793, ss14606597	NT_016354.16:24519586:A:G	NC_000004.12:99103731:A:G	(self)
ss4037154, ss24275294, ss42140463, ss81892438, ss98986597, ss139537326, ss139781314	NT_016354.19:24572603:A:G	NC_000004.12:99103731:A:G	(self)
67794, 9977758346, ss5314500090	NC_000004.12:99103731:A:T	NC_000004.12:99103731:A:T	(self)

Removed from this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Destination RSIDs
ss2433236023	NC_000004.11:100024882:A:T	NC_000004.12:99103731:A:T

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

1 citation for rs2851275

PMID	Title	Author	Year	Journal
19298322	Associations and interactions between SNPs in the alcohol metabolizing genes and alcoholism phenotypes in European Americans.	Sherva R et al.	2009	Alcoholism, clinical and experimental research

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

rs2851275