Name: rs2302490
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.

rs2302490

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr19:2740231 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.460713 (121946/264690, TOPMED)
T=0.451363 (63264/140162, GnomAD)
T=0.36027 (12966/35990, ALFA) (+ 16 more)
C=0.44835 (12664/28246, 14KJPN)
C=0.44817 (7506/16748, 8.3KJPN)
C=0.4560 (2920/6404, 1000G_30x)
C=0.4609 (2308/5008, 1000G)
T=0.3357 (1504/4480, Estonian)
T=0.2948 (1136/3854, ALSPAC)
T=0.2840 (1053/3708, TWINSUK)
C=0.4149 (1214/2926, KOREAN)
C=0.4218 (798/1892, HapMap)
C=0.4395 (799/1818, Korea1K)
T=0.353 (212/600, NorthernSweden)
C=0.300 (125/416, SGDP_PRJ)
T=0.477 (103/216, Qatari)
T=0.495 (106/214, Vietnamese)
T=0.23 (9/40, GENOME_DK)
C=0.45 (18/40, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: SLC39A3 : 2KB Upstream 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	35990	C=0.63973	T=0.36027
European	Sub	28542	C=0.69879	T=0.30121
African	Sub	4312	C=0.2565	T=0.7435
African Others	Sub	158	C=0.152	T=0.848
African American	Sub	4154	C=0.2605	T=0.7395
Asian	Sub	136	C=0.485	T=0.515
East Asian	Sub	108	C=0.509	T=0.491
Other Asian	Sub	28	C=0.39	T=0.61
Latin American 1	Sub	182	C=0.577	T=0.423
Latin American 2	Sub	754	C=0.682	T=0.318
South Asian	Sub	114	C=0.535	T=0.465
Other	Sub	1950	C=0.6292	T=0.3708

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").

Download

Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	C=0.539287	T=0.460713
gnomAD - Genomes	Global	Study-wide	140162	C=0.548637	T=0.451363
gnomAD - Genomes	European	Sub	75894	C=0.69655	T=0.30345
gnomAD - Genomes	African	Sub	42012	C=0.24988	T=0.75012
gnomAD - Genomes	American	Sub	13658	C=0.63897	T=0.36103
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	C=0.6741	T=0.3259
gnomAD - Genomes	East Asian	Sub	3128	C=0.4444	T=0.5556
gnomAD - Genomes	Other	Sub	2150	C=0.5493	T=0.4507
Allele Frequency Aggregator	Total	Global	35990	C=0.63973	T=0.36027
Allele Frequency Aggregator	European	Sub	28542	C=0.69879	T=0.30121
Allele Frequency Aggregator	African	Sub	4312	C=0.2565	T=0.7435
Allele Frequency Aggregator	Other	Sub	1950	C=0.6292	T=0.3708
Allele Frequency Aggregator	Latin American 2	Sub	754	C=0.682	T=0.318
Allele Frequency Aggregator	Latin American 1	Sub	182	C=0.577	T=0.423
Allele Frequency Aggregator	Asian	Sub	136	C=0.485	T=0.515
Allele Frequency Aggregator	South Asian	Sub	114	C=0.535	T=0.465
14KJPN	JAPANESE	Study-wide	28246	C=0.44835	T=0.55165
8.3KJPN	JAPANESE	Study-wide	16748	C=0.44817	T=0.55183
1000Genomes_30x	Global	Study-wide	6404	C=0.4560	T=0.5440
1000Genomes_30x	African	Sub	1786	C=0.1495	T=0.8505
1000Genomes_30x	Europe	Sub	1266	C=0.7006	T=0.2994
1000Genomes_30x	South Asian	Sub	1202	C=0.5025	T=0.4975
1000Genomes_30x	East Asian	Sub	1170	C=0.4179	T=0.5821
1000Genomes_30x	American	Sub	980	C=0.687	T=0.313
1000Genomes	Global	Study-wide	5008	C=0.4609	T=0.5391
1000Genomes	African	Sub	1322	C=0.1558	T=0.8442
1000Genomes	East Asian	Sub	1008	C=0.4256	T=0.5744
1000Genomes	Europe	Sub	1006	C=0.6948	T=0.3052
1000Genomes	South Asian	Sub	978	C=0.500	T=0.500
1000Genomes	American	Sub	694	C=0.699	T=0.301
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.6643	T=0.3357
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.7052	T=0.2948
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.7160	T=0.2840
KOREAN population from KRGDB	KOREAN	Study-wide	2926	C=0.4149	T=0.5851
HapMap	Global	Study-wide	1892	C=0.4218	T=0.5782
HapMap	American	Sub	770	C=0.566	T=0.434
HapMap	African	Sub	692	C=0.188	T=0.812
HapMap	Asian	Sub	254	C=0.457	T=0.543
HapMap	Europe	Sub	176	C=0.659	T=0.341
Korean Genome Project	KOREAN	Study-wide	1818	C=0.4395	T=0.5605
Northern Sweden	ACPOP	Study-wide	600	C=0.647	T=0.353
SGDP_PRJ	Global	Study-wide	416	C=0.300	T=0.700
Qatari	Global	Study-wide	216	C=0.523	T=0.477
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.505	T=0.495
The Danish reference pan genome	Danish	Study-wide	40	C=0.78	T=0.23
Siberian	Global	Study-wide	40	C=0.45	T=0.55

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.2740231C>T
GRCh37.p13 chr 19	NC_000019.9:g.2740229C>T

Gene: SLC39A3, solute carrier family 39 member 3 (minus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
SLC39A3 transcript variant 1	NM_144564.5:c.	N/A	Upstream Transcript Variant
SLC39A3 transcript variant 2	NM_213568.2:c.	N/A	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	C=	T
GRCh38.p14 chr 19	NC_000019.10:g.2740231=	NC_000019.10:g.2740231C>T
GRCh37.p13 chr 19	NC_000019.9:g.2740229=	NC_000019.9:g.2740229C>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#.

77 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	YUSUKE	ss3248773	Sep 28, 2001 (100)
2	BCM_SSAHASNP	ss10922033	Jul 11, 2003 (116)
3	BCM_SSAHASNP	ss14700995	Dec 05, 2003 (119)
4	KYUGEN	ss35074897	May 24, 2005 (125)
5	ILLUMINA	ss75098245	Dec 06, 2007 (129)
6	HGSV	ss84588418	Dec 15, 2007 (130)
7	HGSV	ss85876890	Dec 15, 2007 (130)
8	BCMHGSC_JDW	ss90883247	Mar 24, 2008 (129)
9	1000GENOMES	ss114748971	Jan 25, 2009 (130)
10	KRIBB_YJKIM	ss119430033	Dec 01, 2009 (131)
11	GMI	ss155535118	Dec 01, 2009 (131)
12	COMPLETE_GENOMICS	ss167671326	Jul 04, 2010 (132)
13	COMPLETE_GENOMICS	ss168883248	Jul 04, 2010 (132)
14	ILLUMINA	ss173275631	Jul 04, 2010 (132)
15	BUSHMAN	ss203596991	Jul 04, 2010 (132)
16	1000GENOMES	ss228012029	Jul 14, 2010 (132)
17	1000GENOMES	ss237580688	Jul 15, 2010 (132)
18	1000GENOMES	ss243807485	Jul 15, 2010 (132)
19	GMI	ss283100318	May 04, 2012 (137)
20	ILLUMINA	ss483557473	May 04, 2012 (137)
21	ILLUMINA	ss483808791	May 04, 2012 (137)
22	ILLUMINA	ss535763966	Sep 08, 2015 (146)
23	SSMP	ss661665883	Apr 25, 2013 (138)
24	ILLUMINA	ss779419546	Sep 08, 2015 (146)
25	ILLUMINA	ss782222224	Sep 08, 2015 (146)
26	ILLUMINA	ss834888710	Sep 08, 2015 (146)
27	EVA-GONL	ss994020772	Aug 21, 2014 (142)
28	1000GENOMES	ss1362098301	Aug 21, 2014 (142)
29	DDI	ss1428314202	Apr 01, 2015 (144)
30	EVA_GENOME_DK	ss1578528860	Apr 01, 2015 (144)
31	EVA_UK10K_ALSPAC	ss1637446026	Apr 01, 2015 (144)
32	EVA_UK10K_TWINSUK	ss1680440059	Apr 01, 2015 (144)
33	EVA_DECODE	ss1698083400	Apr 01, 2015 (144)
34	EVA_SVP	ss1713647137	Apr 01, 2015 (144)
35	HAMMER_LAB	ss1809176795	Sep 08, 2015 (146)
36	WEILL_CORNELL_DGM	ss1937498384	Feb 12, 2016 (147)
37	JJLAB	ss2029524301	Sep 14, 2016 (149)
38	USC_VALOUEV	ss2158037759	Dec 20, 2016 (150)
39	HUMAN_LONGEVITY	ss2223777195	Dec 20, 2016 (150)
40	SYSTEMSBIOZJU	ss2629260901	Nov 08, 2017 (151)
41	ILLUMINA	ss2633509982	Nov 08, 2017 (151)
42	GRF	ss2702641259	Nov 08, 2017 (151)
43	GNOMAD	ss2959708664	Nov 08, 2017 (151)
44	SWEGEN	ss3016977544	Nov 08, 2017 (151)
45	CSHL	ss3352164671	Nov 08, 2017 (151)
46	ILLUMINA	ss3627873264	Oct 12, 2018 (152)
47	ILLUMINA	ss3631484136	Oct 12, 2018 (152)
48	ILLUMINA	ss3638211720	Oct 12, 2018 (152)
49	ILLUMINA	ss3643186323	Oct 12, 2018 (152)
50	OMUKHERJEE_ADBS	ss3646526831	Oct 12, 2018 (152)
51	EGCUT_WGS	ss3683825072	Jul 13, 2019 (153)
52	EVA_DECODE	ss3702205522	Jul 13, 2019 (153)
53	ACPOP	ss3742795115	Jul 13, 2019 (153)
54	EVA	ss3755733198	Jul 13, 2019 (153)
55	KHV_HUMAN_GENOMES	ss3820986963	Jul 13, 2019 (153)
56	EVA	ss3835315279	Apr 27, 2020 (154)
57	EVA	ss3841279827	Apr 27, 2020 (154)
58	EVA	ss3846783713	Apr 27, 2020 (154)
59	SGDP_PRJ	ss3887614666	Apr 27, 2020 (154)
60	KRGDB	ss3937547801	Apr 27, 2020 (154)
61	KOGIC	ss3980671912	Apr 27, 2020 (154)
62	EVA	ss4017812387	Apr 26, 2021 (155)
63	TOPMED	ss5065899016	Apr 26, 2021 (155)
64	TOMMO_GENOMICS	ss5226407068	Apr 26, 2021 (155)
65	1000G_HIGH_COVERAGE	ss5306248137	Oct 16, 2022 (156)
66	EVA	ss5315956677	Oct 16, 2022 (156)
67	EVA	ss5433157835	Oct 16, 2022 (156)
68	HUGCELL_USP	ss5498913945	Oct 16, 2022 (156)
69	EVA	ss5512029168	Oct 16, 2022 (156)
70	1000G_HIGH_COVERAGE	ss5611554163	Oct 16, 2022 (156)
71	SANFORD_IMAGENETICS	ss5661844087	Oct 16, 2022 (156)
72	TOMMO_GENOMICS	ss5784568435	Oct 16, 2022 (156)
73	YY_MCH	ss5817346321	Oct 16, 2022 (156)
74	EVA	ss5840161014	Oct 16, 2022 (156)
75	EVA	ss5852177749	Oct 16, 2022 (156)
76	EVA	ss5927044876	Oct 16, 2022 (156)
77	EVA	ss5953273898	Oct 16, 2022 (156)
78	1000Genomes	NC_000019.9 - 2740229	Oct 12, 2018 (152)
79	1000Genomes_30x	NC_000019.10 - 2740231	Oct 16, 2022 (156)
80	The Avon Longitudinal Study of Parents and Children	NC_000019.9 - 2740229	Oct 12, 2018 (152)
81	Genetic variation in the Estonian population	NC_000019.9 - 2740229	Oct 12, 2018 (152)
82	The Danish reference pan genome	NC_000019.9 - 2740229	Apr 27, 2020 (154)
83	gnomAD - Genomes	NC_000019.10 - 2740231	Apr 26, 2021 (155)
84	HapMap	NC_000019.10 - 2740231	Apr 27, 2020 (154)
85	KOREAN population from KRGDB	NC_000019.9 - 2740229	Apr 27, 2020 (154)
86	Korean Genome Project	NC_000019.10 - 2740231	Apr 27, 2020 (154)
87	Northern Sweden	NC_000019.9 - 2740229	Jul 13, 2019 (153)
88	Qatari	NC_000019.9 - 2740229	Apr 27, 2020 (154)
89	SGDP_PRJ	NC_000019.9 - 2740229	Apr 27, 2020 (154)
90	Siberian	NC_000019.9 - 2740229	Apr 27, 2020 (154)
91	8.3KJPN	NC_000019.9 - 2740229	Apr 26, 2021 (155)
92	14KJPN	NC_000019.10 - 2740231	Oct 16, 2022 (156)
93	TopMed	NC_000019.10 - 2740231	Apr 26, 2021 (155)
94	UK 10K study - Twins	NC_000019.9 - 2740229	Oct 12, 2018 (152)
95	A Vietnamese Genetic Variation Database	NC_000019.9 - 2740229	Jul 13, 2019 (153)
96	ALFA	NC_000019.10 - 2740231	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)
rs60204940	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss84588418, ss85876890, ss90883247, ss114748971, ss167671326, ss168883248, ss203596991, ss283100318, ss483808791, ss1698083400, ss1713647137, ss3643186323	NC_000019.8:2691228:C:T	NC_000019.10:2740230:C:T	(self)
75465748, 41826775, 29563320, 4715892, 44725195, 16079980, 19540306, 39631646, 10554113, 84376375, 41826775, 9249483, ss228012029, ss237580688, ss243807485, ss483557473, ss535763966, ss661665883, ss779419546, ss782222224, ss834888710, ss994020772, ss1362098301, ss1428314202, ss1578528860, ss1637446026, ss1680440059, ss1809176795, ss1937498384, ss2029524301, ss2158037759, ss2629260901, ss2633509982, ss2702641259, ss2959708664, ss3016977544, ss3352164671, ss3627873264, ss3631484136, ss3638211720, ss3646526831, ss3683825072, ss3742795115, ss3755733198, ss3835315279, ss3841279827, ss3887614666, ss3937547801, ss4017812387, ss5226407068, ss5315956677, ss5433157835, ss5512029168, ss5661844087, ss5840161014, ss5953273898	NC_000019.9:2740228:C:T	NC_000019.10:2740230:C:T	(self)
99080098, 532202761, 1659489, 37049913, 118405539, 281444680, 2425975315, ss2223777195, ss3702205522, ss3820986963, ss3846783713, ss3980671912, ss5065899016, ss5306248137, ss5498913945, ss5611554163, ss5784568435, ss5817346321, ss5852177749, ss5927044876	NC_000019.10:2740230:C:T	NC_000019.10:2740230:C:T	(self)
ss10922033	NT_011255.13:2680228:C:T	NC_000019.10:2740230:C:T	(self)
ss3248773, ss14700995, ss35074897, ss75098245, ss119430033, ss155535118, ss173275631	NT_011255.14:2680228:C:T	NC_000019.10:2740230:C:T	(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 rs2302490

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

rs2302490