Name: rs11878604
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.

rs11878604

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr19:40827379 (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: C=0.148060 (39190/264690, TOPMED)
C=0.142584 (19558/137168, GnomAD)
C=0.09950 (9126/91714, ALFA) (+ 18 more)
C=0.38729 (10944/28258, 14KJPN)
C=0.38473 (6448/16760, 8.3KJPN)
C=0.2211 (1416/6404, 1000G_30x)
C=0.2190 (1097/5008, 1000G)
C=0.1055 (472/4472, Estonian)
C=0.0664 (256/3854, ALSPAC)
C=0.0744 (276/3708, TWINSUK)
C=0.4201 (1231/2930, KOREAN)
C=0.2422 (497/2052, HGDP_Stanford)
C=0.4050 (742/1832, Korea1K)
C=0.2366 (397/1678, HapMap)
C=0.069 (69/998, GoNL)
C=0.069 (41/598, NorthernSweden)
C=0.171 (37/216, Qatari)
C=0.439 (93/212, Vietnamese)
T=0.422 (81/192, SGDP_PRJ)
C=0.11 (8/76, Ancient Sardinia)
T=0.42 (5/12, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: None
Publications: 2 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	91714	T=0.90050	C=0.09950	0.822601	0.021611	0.155789	32
European	Sub	80464	T=0.91601	C=0.08399	0.848852	0.016827	0.134321	32
African	Sub	6022	T=0.7562	C=0.2438	0.577549	0.065095	0.357356	2
African Others	Sub	222	T=0.694	C=0.306	0.459459	0.072072	0.468468	1
African American	Sub	5800	T=0.7586	C=0.2414	0.582069	0.064828	0.353103	2
Asian	Sub	318	T=0.629	C=0.371	0.377358	0.119497	0.503145	1
East Asian	Sub	228	T=0.592	C=0.408	0.333333	0.149123	0.517544	0
Other Asian	Sub	90	T=0.72	C=0.28	0.488889	0.044444	0.466667	1
Latin American 1	Sub	302	T=0.848	C=0.152	0.735099	0.039735	0.225166	2
Latin American 2	Sub	1942	T=0.8517	C=0.1483	0.742533	0.039135	0.218332	10
South Asian	Sub	128	T=0.750	C=0.250	0.546875	0.046875	0.40625	0
Other	Sub	2538	T=0.8361	C=0.1639	0.71316	0.040977	0.245863	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	T=0.851940	C=0.148060
gnomAD - Genomes	Global	Study-wide	137168	T=0.857416	C=0.142584
gnomAD - Genomes	European	Sub	75452	T=0.91597	C=0.08403
gnomAD - Genomes	African	Sub	39654	T=0.76005	C=0.23995
gnomAD - Genomes	American	Sub	13510	T=0.86366	C=0.13634
gnomAD - Genomes	Ashkenazi Jewish	Sub	3306	T=0.8854	C=0.1146
gnomAD - Genomes	East Asian	Sub	3114	T=0.6249	C=0.3751
gnomAD - Genomes	Other	Sub	2132	T=0.8527	C=0.1473
Allele Frequency Aggregator	Total	Global	91714	T=0.90050	C=0.09950
Allele Frequency Aggregator	European	Sub	80464	T=0.91601	C=0.08399
Allele Frequency Aggregator	African	Sub	6022	T=0.7562	C=0.2438
Allele Frequency Aggregator	Other	Sub	2538	T=0.8361	C=0.1639
Allele Frequency Aggregator	Latin American 2	Sub	1942	T=0.8517	C=0.1483
Allele Frequency Aggregator	Asian	Sub	318	T=0.629	C=0.371
Allele Frequency Aggregator	Latin American 1	Sub	302	T=0.848	C=0.152
Allele Frequency Aggregator	South Asian	Sub	128	T=0.750	C=0.250
14KJPN	JAPANESE	Study-wide	28258	T=0.61271	C=0.38729
8.3KJPN	JAPANESE	Study-wide	16760	T=0.61527	C=0.38473
1000Genomes_30x	Global	Study-wide	6404	T=0.7789	C=0.2211
1000Genomes_30x	African	Sub	1786	T=0.7301	C=0.2699
1000Genomes_30x	Europe	Sub	1266	T=0.9171	C=0.0829
1000Genomes_30x	South Asian	Sub	1202	T=0.7854	C=0.2146
1000Genomes_30x	East Asian	Sub	1170	T=0.6094	C=0.3906
1000Genomes_30x	American	Sub	980	T=0.884	C=0.116
1000Genomes	Global	Study-wide	5008	T=0.7810	C=0.2190
1000Genomes	African	Sub	1322	T=0.7504	C=0.2496
1000Genomes	East Asian	Sub	1008	T=0.6171	C=0.3829
1000Genomes	Europe	Sub	1006	T=0.9155	C=0.0845
1000Genomes	South Asian	Sub	978	T=0.791	C=0.209
1000Genomes	American	Sub	694	T=0.867	C=0.133
Genetic variation in the Estonian population	Estonian	Study-wide	4472	T=0.8945	C=0.1055
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9336	C=0.0664
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9256	C=0.0744
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.5799	C=0.4201
HGDP-CEPH-db Supplement 1	Global	Study-wide	2052	T=0.7578	C=0.2422
HGDP-CEPH-db Supplement 1	Est_Asia	Sub	468	T=0.622	C=0.378
HGDP-CEPH-db Supplement 1	Central_South_Asia	Sub	412	T=0.784	C=0.216
HGDP-CEPH-db Supplement 1	Middle_Est	Sub	340	T=0.850	C=0.150
HGDP-CEPH-db Supplement 1	Europe	Sub	318	T=0.906	C=0.094
HGDP-CEPH-db Supplement 1	Africa	Sub	226	T=0.677	C=0.323
HGDP-CEPH-db Supplement 1	America	Sub	216	T=0.653	C=0.347
HGDP-CEPH-db Supplement 1	Oceania	Sub	72	T=0.97	C=0.03
Korean Genome Project	KOREAN	Study-wide	1832	T=0.5950	C=0.4050
HapMap	Global	Study-wide	1678	T=0.7634	C=0.2366
HapMap	American	Sub	670	T=0.785	C=0.215
HapMap	African	Sub	578	T=0.766	C=0.234
HapMap	Asian	Sub	254	T=0.591	C=0.409
HapMap	Europe	Sub	176	T=0.920	C=0.080
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.931	C=0.069
Northern Sweden	ACPOP	Study-wide	598	T=0.931	C=0.069
Qatari	Global	Study-wide	216	T=0.829	C=0.171
A Vietnamese Genetic Variation Database	Global	Study-wide	212	T=0.561	C=0.439
SGDP_PRJ	Global	Study-wide	192	T=0.422	C=0.578
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	76	T=0.89	C=0.11
Siberian	Global	Study-wide	12	T=0.42	C=0.58

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.40827379T>C
GRCh37.p13 chr 19	NC_000019.9:g.41333284T>C

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 19	NC_000019.10:g.40827379=	NC_000019.10:g.40827379T>C
GRCh37.p13 chr 19	NC_000019.9:g.41333284=	NC_000019.9:g.41333284T>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#.

100 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	CSHL-HAPMAP	ss17613370	Feb 28, 2004 (120)
2	ABI	ss44177122	Mar 13, 2006 (126)
3	ILLUMINA	ss66668954	Nov 30, 2006 (127)
4	ILLUMINA	ss66964217	Nov 30, 2006 (127)
5	ILLUMINA	ss67130673	Nov 30, 2006 (127)
6	ILLUMINA	ss70401476	May 17, 2007 (127)
7	ILLUMINA	ss70546470	May 26, 2008 (130)
8	ILLUMINA	ss71080202	May 17, 2007 (127)
9	ILLUMINA	ss75607306	Dec 06, 2007 (129)
10	HGSV	ss83813746	Dec 15, 2007 (130)
11	KRIBB_YJKIM	ss85154836	Dec 15, 2007 (130)
12	ILLUMINA	ss121515774	Dec 01, 2009 (131)
13	ILLUMINA	ss153082822	Dec 01, 2009 (131)
14	GMI	ss155906979	Dec 01, 2009 (131)
15	ILLUMINA	ss159194002	Dec 01, 2009 (131)
16	ILLUMINA	ss160013272	Dec 01, 2009 (131)
17	ENSEMBL	ss161879239	Dec 01, 2009 (131)
18	ILLUMINA	ss169985825	Jul 04, 2010 (132)
19	ILLUMINA	ss171674703	Jul 04, 2010 (132)
20	BUSHMAN	ss203756293	Jul 04, 2010 (132)
21	BCM-HGSC-SUB	ss208427418	Jul 04, 2010 (132)
22	1000GENOMES	ss211964883	Jul 14, 2010 (132)
23	GMI	ss283212387	May 04, 2012 (137)
24	PJP	ss292178726	May 09, 2011 (134)
25	1000GENOMES	ss465596343	Sep 17, 2011 (135)
26	ILLUMINA	ss479617881	May 04, 2012 (137)
27	ILLUMINA	ss479623084	May 04, 2012 (137)
28	ILLUMINA	ss480118807	Sep 08, 2015 (146)
29	ILLUMINA	ss484607734	May 04, 2012 (137)
30	ILLUMINA	ss536733055	Sep 08, 2015 (146)
31	TISHKOFF	ss565987772	Apr 25, 2013 (138)
32	ILLUMINA	ss782750667	Sep 08, 2015 (146)
33	ILLUMINA	ss783717347	Sep 08, 2015 (146)
34	ILLUMINA	ss825370784	Jul 19, 2016 (147)
35	ILLUMINA	ss832002779	Sep 08, 2015 (146)
36	ILLUMINA	ss832706475	Jul 13, 2019 (153)
37	ILLUMINA	ss836165308	Sep 08, 2015 (146)
38	EVA-GONL	ss994307501	Aug 21, 2014 (142)
39	JMKIDD_LAB	ss1081909311	Aug 21, 2014 (142)
40	1000GENOMES	ss1363195583	Aug 21, 2014 (142)
41	DDI	ss1428405104	Apr 01, 2015 (144)
42	EVA_UK10K_ALSPAC	ss1637984486	Apr 01, 2015 (144)
43	EVA_UK10K_TWINSUK	ss1680978519	Apr 01, 2015 (144)
44	EVA_DECODE	ss1698361414	Apr 01, 2015 (144)
45	EVA_SVP	ss1713663194	Apr 01, 2015 (144)
46	ILLUMINA	ss1752285762	Sep 08, 2015 (146)
47	HAMMER_LAB	ss1809311113	Sep 08, 2015 (146)
48	WEILL_CORNELL_DGM	ss1937801079	Feb 12, 2016 (147)
49	ILLUMINA	ss1959865081	Feb 12, 2016 (147)
50	JJLAB	ss2029679966	Sep 14, 2016 (149)
51	USC_VALOUEV	ss2158220871	Dec 20, 2016 (150)
52	HUMAN_LONGEVITY	ss2225828799	Dec 20, 2016 (150)
53	SYSTEMSBIOZJU	ss2629337110	Nov 08, 2017 (151)
54	ILLUMINA	ss2633540908	Nov 08, 2017 (151)
55	GRF	ss2702831494	Nov 08, 2017 (151)
56	GNOMAD	ss2962957937	Nov 08, 2017 (151)
57	AFFY	ss2985772396	Nov 08, 2017 (151)
58	SWEGEN	ss3017486058	Nov 08, 2017 (151)
59	ILLUMINA	ss3021906834	Nov 08, 2017 (151)
60	BIOINF_KMB_FNS_UNIBA	ss3028671627	Nov 08, 2017 (151)
61	ILLUMINA	ss3631512273	Oct 12, 2018 (152)
62	ILLUMINA	ss3633180565	Oct 12, 2018 (152)
63	ILLUMINA	ss3633891004	Oct 12, 2018 (152)
64	ILLUMINA	ss3634735984	Oct 12, 2018 (152)
65	ILLUMINA	ss3636423270	Oct 12, 2018 (152)
66	ILLUMINA	ss3638227836	Oct 12, 2018 (152)
67	ILLUMINA	ss3639119980	Oct 12, 2018 (152)
68	ILLUMINA	ss3639570606	Oct 12, 2018 (152)
69	ILLUMINA	ss3640443292	Oct 12, 2018 (152)
70	ILLUMINA	ss3643200708	Oct 12, 2018 (152)
71	ILLUMINA	ss3652332803	Oct 12, 2018 (152)
72	EGCUT_WGS	ss3684252242	Jul 13, 2019 (153)
73	EVA_DECODE	ss3702784207	Jul 13, 2019 (153)
74	ACPOP	ss3743046093	Jul 13, 2019 (153)
75	ILLUMINA	ss3745036000	Jul 13, 2019 (153)
76	EVA	ss3756074004	Jul 13, 2019 (153)
77	ILLUMINA	ss3772533125	Jul 13, 2019 (153)
78	KHV_HUMAN_GENOMES	ss3821321832	Jul 13, 2019 (153)
79	EVA	ss3835466140	Apr 27, 2020 (154)
80	EVA	ss3841355520	Apr 27, 2020 (154)
81	EVA	ss3846861405	Apr 27, 2020 (154)
82	HGDP	ss3847599723	Apr 27, 2020 (154)
83	SGDP_PRJ	ss3888233294	Apr 27, 2020 (154)
84	KRGDB	ss3938350189	Apr 27, 2020 (154)
85	KOGIC	ss3981368424	Apr 27, 2020 (154)
86	EVA	ss3985855040	Apr 26, 2021 (155)
87	EVA	ss4017825241	Apr 26, 2021 (155)
88	TOPMED	ss5075098816	Apr 26, 2021 (155)
89	TOMMO_GENOMICS	ss5227797766	Apr 26, 2021 (155)
90	1000G_HIGH_COVERAGE	ss5307275503	Oct 16, 2022 (156)
91	EVA	ss5434891520	Oct 16, 2022 (156)
92	HUGCELL_USP	ss5499797749	Oct 16, 2022 (156)
93	1000G_HIGH_COVERAGE	ss5613019415	Oct 16, 2022 (156)
94	SANFORD_IMAGENETICS	ss5662407349	Oct 16, 2022 (156)
95	TOMMO_GENOMICS	ss5786443752	Oct 16, 2022 (156)
96	YY_MCH	ss5817608921	Oct 16, 2022 (156)
97	EVA	ss5852293636	Oct 16, 2022 (156)
98	EVA	ss5928134570	Oct 16, 2022 (156)
99	EVA	ss5953821847	Oct 16, 2022 (156)
100	EVA	ss5981054150	Oct 16, 2022 (156)
101	1000Genomes	NC_000019.9 - 41333284	Oct 12, 2018 (152)
102	1000Genomes_30x	NC_000019.10 - 40827379	Oct 16, 2022 (156)
103	The Avon Longitudinal Study of Parents and Children	NC_000019.9 - 41333284	Oct 12, 2018 (152)
104	Genetic variation in the Estonian population	NC_000019.9 - 41333284	Oct 12, 2018 (152)
105	gnomAD - Genomes	NC_000019.10 - 40827379	Apr 26, 2021 (155)
106	Genome of the Netherlands Release 5	NC_000019.9 - 41333284	Apr 27, 2020 (154)
107	HGDP-CEPH-db Supplement 1	NC_000019.8 - 46025124	Apr 27, 2020 (154)
108	HapMap	NC_000019.10 - 40827379	Apr 27, 2020 (154)
109	KOREAN population from KRGDB	NC_000019.9 - 41333284	Apr 27, 2020 (154)
110	Korean Genome Project	NC_000019.10 - 40827379	Apr 27, 2020 (154)
111	Northern Sweden	NC_000019.9 - 41333284	Jul 13, 2019 (153)
112	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000019.9 - 41333284	Apr 26, 2021 (155)
113	Qatari	NC_000019.9 - 41333284	Apr 27, 2020 (154)
114	SGDP_PRJ	NC_000019.9 - 41333284	Apr 27, 2020 (154)
115	Siberian	NC_000019.9 - 41333284	Apr 27, 2020 (154)
116	8.3KJPN	NC_000019.9 - 41333284	Apr 26, 2021 (155)
117	14KJPN	NC_000019.10 - 40827379	Oct 16, 2022 (156)
118	TopMed	NC_000019.10 - 40827379	Apr 26, 2021 (155)
119	UK 10K study - Twins	NC_000019.9 - 41333284	Oct 12, 2018 (152)
120	A Vietnamese Genetic Variation Database	NC_000019.9 - 41333284	Jul 13, 2019 (153)
121	ALFA	NC_000019.10 - 40827379	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)
rs60902413	May 26, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
277615, ss83813746, ss203756293, ss208427418, ss211964883, ss283212387, ss292178726, ss479617881, ss825370784, ss1698361414, ss1713663194, ss3639119980, ss3639570606, ss3643200708, ss3847599723	NC_000019.8:46025123:T:C	NC_000019.10:40827378:T:C	(self)
76604080, 42428226, 29990490, 18900444, 45527583, 16330958, 1080967, 19843001, 40250274, 10737225, 85767073, 42428226, 9371370, ss465596343, ss479623084, ss480118807, ss484607734, ss536733055, ss565987772, ss782750667, ss783717347, ss832002779, ss832706475, ss836165308, ss994307501, ss1081909311, ss1363195583, ss1428405104, ss1637984486, ss1680978519, ss1752285762, ss1809311113, ss1937801079, ss1959865081, ss2029679966, ss2158220871, ss2629337110, ss2633540908, ss2702831494, ss2962957937, ss2985772396, ss3017486058, ss3021906834, ss3631512273, ss3633180565, ss3633891004, ss3634735984, ss3636423270, ss3638227836, ss3640443292, ss3652332803, ss3684252242, ss3743046093, ss3745036000, ss3756074004, ss3772533125, ss3835466140, ss3841355520, ss3888233294, ss3938350189, ss3985855040, ss4017825241, ss5227797766, ss5434891520, ss5662407349, ss5953821847, ss5981054150	NC_000019.9:41333283:T:C	NC_000019.10:40827378:T:C	(self)
100545350, 540281090, 1697222, 37746425, 120280856, 290644480, 4417509920, ss2225828799, ss3028671627, ss3702784207, ss3821321832, ss3846861405, ss3981368424, ss5075098816, ss5307275503, ss5499797749, ss5613019415, ss5786443752, ss5817608921, ss5852293636, ss5928134570	NC_000019.10:40827378:T:C	NC_000019.10:40827378:T:C	(self)
ss17613370	NT_011109.15:13601501:T:C	NC_000019.10:40827378:T:C	(self)
ss44177122, ss66668954, ss66964217, ss67130673, ss70401476, ss70546470, ss71080202, ss75607306, ss85154836, ss121515774, ss153082822, ss155906979, ss159194002, ss160013272, ss161879239, ss169985825, ss171674703	NT_011109.16:13601501:T:C	NC_000019.10:40827378:T:C	(self)

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

2 citations for rs11878604

PMID	Title	Author	Year	Journal
27166759	Converging findings from linkage and association analyses on susceptibility genes for smoking and other addictions.	Yang J et al.	2016	Molecular psychiatry
34599228	Analyses of nicotine metabolism biomarker genetics stratified by sex in African and European Americans.	Chenoweth MJ et al.	2021	Scientific reports

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

rs11878604