Name: rs459
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.

rs459

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr7:97802035 (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=0.098239 (26003/264690, TOPMED)
T=0.099078 (13882/140112, GnomAD)
T=0.13373 (3779/28258, 14KJPN) (+ 18 more)
T=0.11398 (2567/22522, ALFA)
T=0.13241 (2219/16758, 8.3KJPN)
T=0.1163 (745/6404, 1000G_30x)
T=0.1206 (604/5008, 1000G)
T=0.1408 (631/4480, Estonian)
T=0.1292 (498/3854, ALSPAC)
T=0.1343 (498/3708, TWINSUK)
T=0.1222 (358/2930, KOREAN)
T=0.1053 (193/1832, Korea1K)
T=0.0772 (132/1710, HapMap)
T=0.132 (132/998, GoNL)
T=0.130 (78/600, NorthernSweden)
T=0.153 (33/216, Qatari)
T=0.093 (20/216, Vietnamese)
C=0.420 (47/112, SGDP_PRJ)
T=0.12 (5/40, GENOME_DK)
C=0.50 (11/22, Siberian)
T=0.50 (11/22, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: None
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	22522	C=0.88602	T=0.11398
European	Sub	16438	C=0.86732	T=0.13268
African	Sub	4082	C=0.9667	T=0.0333
African Others	Sub	144	C=1.000	T=0.000
African American	Sub	3938	C=0.9655	T=0.0345
Asian	Sub	116	C=0.914	T=0.086
East Asian	Sub	88	C=0.91	T=0.09
Other Asian	Sub	28	C=0.93	T=0.07
Latin American 1	Sub	154	C=0.838	T=0.162
Latin American 2	Sub	616	C=0.904	T=0.096
South Asian	Sub	98	C=0.74	T=0.26
Other	Sub	1018	C=0.8713	T=0.1287

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=0.901761	T=0.098239
gnomAD - Genomes	Global	Study-wide	140112	C=0.900922	T=0.099078
gnomAD - Genomes	European	Sub	75852	C=0.86753	T=0.13247
gnomAD - Genomes	African	Sub	42014	C=0.96511	T=0.03489
gnomAD - Genomes	American	Sub	13644	C=0.90120	T=0.09880
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	C=0.8364	T=0.1636
gnomAD - Genomes	East Asian	Sub	3130	C=0.9192	T=0.0808
gnomAD - Genomes	Other	Sub	2152	C=0.8959	T=0.1041
14KJPN	JAPANESE	Study-wide	28258	C=0.86627	T=0.13373
Allele Frequency Aggregator	Total	Global	22522	C=0.88602	T=0.11398
Allele Frequency Aggregator	European	Sub	16438	C=0.86732	T=0.13268
Allele Frequency Aggregator	African	Sub	4082	C=0.9667	T=0.0333
Allele Frequency Aggregator	Other	Sub	1018	C=0.8713	T=0.1287
Allele Frequency Aggregator	Latin American 2	Sub	616	C=0.904	T=0.096
Allele Frequency Aggregator	Latin American 1	Sub	154	C=0.838	T=0.162
Allele Frequency Aggregator	Asian	Sub	116	C=0.914	T=0.086
Allele Frequency Aggregator	South Asian	Sub	98	C=0.74	T=0.26
8.3KJPN	JAPANESE	Study-wide	16758	C=0.86759	T=0.13241
1000Genomes_30x	Global	Study-wide	6404	C=0.8837	T=0.1163
1000Genomes_30x	African	Sub	1786	C=0.9787	T=0.0213
1000Genomes_30x	Europe	Sub	1266	C=0.8728	T=0.1272
1000Genomes_30x	South Asian	Sub	1202	C=0.7404	T=0.2596
1000Genomes_30x	East Asian	Sub	1170	C=0.9034	T=0.0966
1000Genomes_30x	American	Sub	980	C=0.877	T=0.123
1000Genomes	Global	Study-wide	5008	C=0.8794	T=0.1206
1000Genomes	African	Sub	1322	C=0.9766	T=0.0234
1000Genomes	East Asian	Sub	1008	C=0.9038	T=0.0962
1000Genomes	Europe	Sub	1006	C=0.8648	T=0.1352
1000Genomes	South Asian	Sub	978	C=0.739	T=0.261
1000Genomes	American	Sub	694	C=0.878	T=0.122
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.8592	T=0.1408
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.8708	T=0.1292
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.8657	T=0.1343
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.8778	T=0.1222
Korean Genome Project	KOREAN	Study-wide	1832	C=0.8947	T=0.1053
HapMap	Global	Study-wide	1710	C=0.9228	T=0.0772
HapMap	African	Sub	690	C=0.964	T=0.036
HapMap	American	Sub	592	C=0.909	T=0.091
HapMap	Asian	Sub	254	C=0.894	T=0.106
HapMap	Europe	Sub	174	C=0.851	T=0.149
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.868	T=0.132
Northern Sweden	ACPOP	Study-wide	600	C=0.870	T=0.130
Qatari	Global	Study-wide	216	C=0.847	T=0.153
A Vietnamese Genetic Variation Database	Global	Study-wide	216	C=0.907	T=0.093
SGDP_PRJ	Global	Study-wide	112	C=0.420	T=0.580
The Danish reference pan genome	Danish	Study-wide	40	C=0.88	T=0.12
Siberian	Global	Study-wide	22	C=0.50	T=0.50

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 7	NC_000007.14:g.97802035C>T
GRCh37.p13 chr 7	NC_000007.13:g.97431347C>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=	T
GRCh38.p14 chr 7	NC_000007.14:g.97802035=	NC_000007.14:g.97802035C>T
GRCh37.p13 chr 7	NC_000007.13:g.97431347=	NC_000007.13:g.97431347C>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#.

64 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	KWOK	ss463	Sep 19, 2000 (36)
2	ABI	ss43066867	Mar 13, 2006 (126)
3	ILLUMINA	ss75248836	Dec 07, 2007 (129)
4	KRIBB_YJKIM	ss80753379	Dec 16, 2007 (130)
5	KRIBB_YJKIM	ss119336855	Dec 01, 2009 (131)
6	COMPLETE_GENOMICS	ss166895581	Jul 04, 2010 (132)
7	ILLUMINA	ss173757728	Jul 04, 2010 (132)
8	1000GENOMES	ss234088472	Jul 15, 2010 (132)
9	1000GENOMES	ss241021856	Jul 15, 2010 (132)
10	BL	ss254536335	May 09, 2011 (134)
11	GMI	ss279452054	May 04, 2012 (137)
12	ILLUMINA	ss537248022	Sep 08, 2015 (146)
13	TISHKOFF	ss560176118	Apr 25, 2013 (138)
14	SSMP	ss654577638	Apr 25, 2013 (138)
15	EVA-GONL	ss984577033	Aug 21, 2014 (142)
16	JMKIDD_LAB	ss1074822857	Aug 21, 2014 (142)
17	1000GENOMES	ss1326285202	Aug 21, 2014 (142)
18	DDI	ss1431218693	Apr 01, 2015 (144)
19	EVA_GENOME_DK	ss1582320089	Apr 01, 2015 (144)
20	EVA_DECODE	ss1594155714	Apr 01, 2015 (144)
21	EVA_UK10K_ALSPAC	ss1618773002	Apr 01, 2015 (144)
22	EVA_UK10K_TWINSUK	ss1661767035	Apr 01, 2015 (144)
23	EVA_SVP	ss1712973676	Apr 01, 2015 (144)
24	HAMMER_LAB	ss1805127677	Sep 08, 2015 (146)
25	WEILL_CORNELL_DGM	ss1927837235	Feb 12, 2016 (147)
26	GENOMED	ss1970768991	Jul 19, 2016 (147)
27	JJLAB	ss2024601553	Sep 14, 2016 (149)
28	USC_VALOUEV	ss2152822913	Dec 20, 2016 (150)
29	HUMAN_LONGEVITY	ss2296100552	Dec 20, 2016 (150)
30	SYSTEMSBIOZJU	ss2626793064	Nov 08, 2017 (151)
31	GRF	ss2708532798	Nov 08, 2017 (151)
32	GNOMAD	ss2856608835	Nov 08, 2017 (151)
33	SWEGEN	ss3001684407	Nov 08, 2017 (151)
34	BIOINF_KMB_FNS_UNIBA	ss3026093776	Nov 08, 2017 (151)
35	CSHL	ss3347746192	Nov 08, 2017 (151)
36	ILLUMINA	ss3629870344	Oct 12, 2018 (152)
37	ILLUMINA	ss3638712360	Oct 12, 2018 (152)
38	ILLUMINA	ss3643646993	Oct 12, 2018 (152)
39	URBANLAB	ss3648708127	Oct 12, 2018 (152)
40	EGCUT_WGS	ss3669444326	Jul 13, 2019 (153)
41	EVA_DECODE	ss3720272468	Jul 13, 2019 (153)
42	ACPOP	ss3734890892	Jul 13, 2019 (153)
43	EVA	ss3766909306	Jul 13, 2019 (153)
44	KHV_HUMAN_GENOMES	ss3810081861	Jul 13, 2019 (153)
45	EVA	ss3830715900	Apr 26, 2020 (154)
46	EVA	ss3838856857	Apr 26, 2020 (154)
47	EVA	ss3844311913	Apr 26, 2020 (154)
48	SGDP_PRJ	ss3867954058	Apr 26, 2020 (154)
49	KRGDB	ss3915235702	Apr 26, 2020 (154)
50	KOGIC	ss3962157124	Apr 26, 2020 (154)
51	EVA	ss4017349210	Apr 26, 2021 (155)
52	TOPMED	ss4756107027	Apr 26, 2021 (155)
53	TOMMO_GENOMICS	ss5184595889	Apr 26, 2021 (155)
54	1000G_HIGH_COVERAGE	ss5273981570	Oct 13, 2022 (156)
55	HUGCELL_USP	ss5470959066	Oct 13, 2022 (156)
56	EVA	ss5509060048	Oct 13, 2022 (156)
57	1000G_HIGH_COVERAGE	ss5562741161	Oct 13, 2022 (156)
58	SANFORD_IMAGENETICS	ss5643560789	Oct 13, 2022 (156)
59	TOMMO_GENOMICS	ss5725283131	Oct 13, 2022 (156)
60	YY_MCH	ss5808913718	Oct 13, 2022 (156)
61	EVA	ss5823237178	Oct 13, 2022 (156)
62	EVA	ss5856016783	Oct 13, 2022 (156)
63	EVA	ss5860033645	Oct 13, 2022 (156)
64	EVA	ss5972745087	Oct 13, 2022 (156)
65	1000Genomes	NC_000007.13 - 97431347	Oct 12, 2018 (152)
66	1000Genomes_30x	NC_000007.14 - 97802035	Oct 13, 2022 (156)
67	The Avon Longitudinal Study of Parents and Children	NC_000007.13 - 97431347	Oct 12, 2018 (152)
68	Genetic variation in the Estonian population	NC_000007.13 - 97431347	Oct 12, 2018 (152)
69	The Danish reference pan genome	NC_000007.13 - 97431347	Apr 26, 2020 (154)
70	gnomAD - Genomes	NC_000007.14 - 97802035	Apr 26, 2021 (155)
71	Genome of the Netherlands Release 5	NC_000007.13 - 97431347	Apr 26, 2020 (154)
72	HapMap	NC_000007.14 - 97802035	Apr 26, 2020 (154)
73	KOREAN population from KRGDB	NC_000007.13 - 97431347	Apr 26, 2020 (154)
74	Korean Genome Project	NC_000007.14 - 97802035	Apr 26, 2020 (154)
75	Northern Sweden	NC_000007.13 - 97431347	Jul 13, 2019 (153)
76	Qatari	NC_000007.13 - 97431347	Apr 26, 2020 (154)
77	SGDP_PRJ	NC_000007.13 - 97431347	Apr 26, 2020 (154)
78	Siberian	NC_000007.13 - 97431347	Apr 26, 2020 (154)
79	8.3KJPN	NC_000007.13 - 97431347	Apr 26, 2021 (155)
80	14KJPN	NC_000007.14 - 97802035	Oct 13, 2022 (156)
81	TopMed	NC_000007.14 - 97802035	Apr 26, 2021 (155)
82	UK 10K study - Twins	NC_000007.13 - 97431347	Oct 12, 2018 (152)
83	A Vietnamese Genetic Variation Database	NC_000007.13 - 97431347	Jul 13, 2019 (153)
84	ALFA	NC_000007.14 - 97802035	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)
rs61236875	May 26, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss166895581, ss254536335, ss279452054, ss1594155714, ss1712973676, ss3643646993	NC_000007.12:97269282:C:T	NC_000007.14:97802034:C:T	(self)
38297019, 21311428, 15182574, 8485028, 9514598, 22413096, 8175757, 9879165, 19971038, 5339267, 42565196, 21311428, 4753362, ss234088472, ss241021856, ss537248022, ss560176118, ss654577638, ss984577033, ss1074822857, ss1326285202, ss1431218693, ss1582320089, ss1618773002, ss1661767035, ss1805127677, ss1927837235, ss1970768991, ss2024601553, ss2152822913, ss2626793064, ss2708532798, ss2856608835, ss3001684407, ss3347746192, ss3629870344, ss3638712360, ss3669444326, ss3734890892, ss3766909306, ss3830715900, ss3838856857, ss3867954058, ss3915235702, ss4017349210, ss5184595889, ss5509060048, ss5643560789, ss5823237178, ss5972745087	NC_000007.13:97431346:C:T	NC_000007.14:97802034:C:T	(self)
50267096, 270235012, 3453466, 18535125, 59120235, 593484586, 2841869880, ss2296100552, ss3026093776, ss3648708127, ss3720272468, ss3810081861, ss3844311913, ss3962157124, ss4756107027, ss5273981570, ss5470959066, ss5562741161, ss5725283131, ss5808913718, ss5856016783, ss5860033645	NC_000007.14:97802034:C:T	NC_000007.14:97802034:C:T	(self)
ss463, ss43066867, ss75248836, ss80753379, ss119336855, ss173757728	NT_007933.15:35464189:C:T	NC_000007.14:97802034: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 rs459

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

rs459