Name: rs362302
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.

rs362302

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:3241193 (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=0.022978 (6082/264690, TOPMED)
T=0.021621 (3033/140280, GnomAD)
T=0.009353 (1216/130006, ALFA) (+ 11 more)
T=0.0186 (119/6404, 1000G_30x)
T=0.0174 (87/5008, 1000G)
T=0.0018 (8/4480, Estonian)
T=0.0067 (26/3854, ALSPAC)
T=0.0049 (18/3708, TWINSUK)
T=0.0206 (30/1458, HapMap)
T=0.009 (9/998, GoNL)
T=0.013 (8/626, Chileans)
T=0.005 (1/216, Qatari)
C=0.50 (8/16, SGDP_PRJ)
T=0.50 (8/16, SGDP_PRJ)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: HTT : 3 Prime UTR 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: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	130006	C=0.990647	T=0.009353
European	Sub	115058	C=0.993586	T=0.006414
African	Sub	6984	C=0.9416	T=0.0584
African Others	Sub	232	C=0.940	T=0.060
African American	Sub	6752	C=0.9416	T=0.0584
Asian	Sub	506	C=1.000	T=0.000
East Asian	Sub	406	C=1.000	T=0.000
Other Asian	Sub	100	C=1.00	T=0.00
Latin American 1	Sub	606	C=0.988	T=0.012
Latin American 2	Sub	1092	C=0.9927	T=0.0073
South Asian	Sub	190	C=0.989	T=0.011
Other	Sub	5570	C=0.9905	T=0.0095

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=0.977022	T=0.022978
gnomAD - Genomes	Global	Study-wide	140280	C=0.978379	T=0.021621
gnomAD - Genomes	European	Sub	75972	C=0.99501	T=0.00499
gnomAD - Genomes	African	Sub	42038	C=0.94212	T=0.05788
gnomAD - Genomes	American	Sub	13660	C=0.99004	T=0.00996
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.9868	T=0.0132
gnomAD - Genomes	East Asian	Sub	3134	C=0.9997	T=0.0003
gnomAD - Genomes	Other	Sub	2152	C=0.9814	T=0.0186
Allele Frequency Aggregator	Total	Global	130006	C=0.990647	T=0.009353
Allele Frequency Aggregator	European	Sub	115058	C=0.993586	T=0.006414
Allele Frequency Aggregator	African	Sub	6984	C=0.9416	T=0.0584
Allele Frequency Aggregator	Other	Sub	5570	C=0.9905	T=0.0095
Allele Frequency Aggregator	Latin American 2	Sub	1092	C=0.9927	T=0.0073
Allele Frequency Aggregator	Latin American 1	Sub	606	C=0.988	T=0.012
Allele Frequency Aggregator	Asian	Sub	506	C=1.000	T=0.000
Allele Frequency Aggregator	South Asian	Sub	190	C=0.989	T=0.011
1000Genomes_30x	Global	Study-wide	6404	C=0.9814	T=0.0186
1000Genomes_30x	African	Sub	1786	C=0.9496	T=0.0504
1000Genomes_30x	Europe	Sub	1266	C=0.9929	T=0.0071
1000Genomes_30x	South Asian	Sub	1202	C=0.9958	T=0.0042
1000Genomes_30x	East Asian	Sub	1170	C=1.0000	T=0.0000
1000Genomes_30x	American	Sub	980	C=0.985	T=0.015
1000Genomes	Global	Study-wide	5008	C=0.9826	T=0.0174
1000Genomes	African	Sub	1322	C=0.9493	T=0.0507
1000Genomes	East Asian	Sub	1008	C=1.0000	T=0.0000
1000Genomes	Europe	Sub	1006	C=0.9930	T=0.0070
1000Genomes	South Asian	Sub	978	C=0.997	T=0.003
1000Genomes	American	Sub	694	C=0.986	T=0.014
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9982	T=0.0018
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9933	T=0.0067
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9951	T=0.0049
HapMap	Global	Study-wide	1458	C=0.9794	T=0.0206
HapMap	African	Sub	692	C=0.964	T=0.036
HapMap	American	Sub	500	C=0.992	T=0.008
HapMap	Europe	Sub	176	C=0.994	T=0.006
HapMap	Asian	Sub	90	C=1.00	T=0.00
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.991	T=0.009
Chileans	Chilean	Study-wide	626	C=0.987	T=0.013
Qatari	Global	Study-wide	216	C=0.995	T=0.005
SGDP_PRJ	Global	Study-wide	16	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 4	NC_000004.12:g.3241193C>T
GRCh37.p13 chr 4	NC_000004.11:g.3242920C>T
HTT RefSeqGene (LRG_763)	NG_009378.1:g.171519C>T

Gene: HTT, huntingtin (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
HTT transcript variant 2	NM_002111.8:c.*1134=	N/A	3 Prime UTR Variant
HTT transcript variant 1	NM_001388492.1:c.*1134=	N/A	3 Prime UTR 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 4	NC_000004.12:g.3241193=	NC_000004.12:g.3241193C>T
GRCh37.p13 chr 4	NC_000004.11:g.3242920=	NC_000004.11:g.3242920C>T
HTT RefSeqGene (LRG_763)	NG_009378.1:g.171519=	NG_009378.1:g.171519C>T
HTT transcript variant 2	NM_002111.8:c.*1134=	NM_002111.8:c.*1134C>T
HTT transcript	NM_002111.7:c.*1134=	NM_002111.7:c.*1134C>T
HTT transcript	NM_002111.6:c.*1134=	NM_002111.6:c.*1134C>T
HTT transcript variant 1	NM_001388492.1:c.*1134=	NM_001388492.1:c.*1134C>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#.

70 SubSNP, 13 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	ACEVAN	ss459746	Jul 12, 2000 (79)
2	ACEVAN	ss4254639	Jan 04, 2002 (102)
3	PERLEGEN	ss23250284	Sep 20, 2004 (123)
4	ILLUMINA	ss75145787	Dec 07, 2007 (129)
5	AFFY	ss76614837	Dec 07, 2007 (129)
6	ILLUMINA-UK	ss116841450	Feb 14, 2009 (130)
7	KRIBB_YJKIM	ss119351612	Dec 01, 2009 (131)
8	ILLUMINA	ss160630757	Dec 01, 2009 (131)
9	ILLUMINA	ss173609356	Jul 04, 2010 (132)
10	BUSHMAN	ss197915409	Jul 04, 2010 (132)
11	1000GENOMES	ss220699699	Jul 14, 2010 (132)
12	ILLUMINA	ss479709617	May 04, 2012 (137)
13	ILLUMINA	ss480797707	May 04, 2012 (137)
14	ILLUMINA	ss480813397	May 04, 2012 (137)
15	ILLUMINA	ss481737949	Sep 08, 2015 (146)
16	ILLUMINA	ss484804198	May 04, 2012 (137)
17	ILLUMINA	ss485193619	May 04, 2012 (137)
18	ILLUMINA	ss533214639	Sep 08, 2015 (146)
19	TISHKOFF	ss557261838	Apr 25, 2013 (138)
20	ILLUMINA	ss779167759	Sep 08, 2015 (146)
21	ILLUMINA	ss781049065	Sep 08, 2015 (146)
22	ILLUMINA	ss783042866	Aug 21, 2014 (142)
23	ILLUMINA	ss832300624	Apr 01, 2015 (144)
24	ILLUMINA	ss834632885	Sep 08, 2015 (146)
25	EVA-GONL	ss979685318	Aug 21, 2014 (142)
26	JMKIDD_LAB	ss1071222712	Aug 21, 2014 (142)
27	1000GENOMES	ss1308139853	Aug 21, 2014 (142)
28	EVA_DECODE	ss1589181505	Apr 01, 2015 (144)
29	EVA_UK10K_ALSPAC	ss1609262823	Apr 01, 2015 (144)
30	EVA_UK10K_TWINSUK	ss1652256856	Apr 01, 2015 (144)
31	EVA_SVP	ss1712646342	Apr 01, 2015 (144)
32	ILLUMINA	ss1752519562	Sep 08, 2015 (146)
33	HAMMER_LAB	ss1800830939	Sep 08, 2015 (146)
34	WEILL_CORNELL_DGM	ss1922916869	Feb 12, 2016 (147)
35	JJLAB	ss2022031980	Sep 14, 2016 (149)
36	HUMAN_LONGEVITY	ss2259935375	Dec 20, 2016 (150)
37	ILLUMINA	ss2634072304	Nov 08, 2017 (151)
38	ILLUMINA	ss2634072305	Nov 08, 2017 (151)
39	GNOMAD	ss2804837793	Nov 08, 2017 (151)
40	AFFY	ss2985906839	Nov 08, 2017 (151)
41	SWEGEN	ss2994013216	Nov 08, 2017 (151)
42	CSHL	ss3345503812	Nov 08, 2017 (151)
43	ILLUMINA	ss3628886339	Oct 12, 2018 (152)
44	ILLUMINA	ss3632011734	Oct 12, 2018 (152)
45	ILLUMINA	ss3633323543	Oct 12, 2018 (152)
46	ILLUMINA	ss3634042017	Oct 12, 2018 (152)
47	ILLUMINA	ss3634937851	Oct 12, 2018 (152)
48	ILLUMINA	ss3635725224	Oct 12, 2018 (152)
49	ILLUMINA	ss3636636408	Oct 12, 2018 (152)
50	ILLUMINA	ss3637477692	Oct 12, 2018 (152)
51	ILLUMINA	ss3638468255	Oct 12, 2018 (152)
52	ILLUMINA	ss3640645147	Oct 12, 2018 (152)
53	ILLUMINA	ss3643421123	Oct 12, 2018 (152)
54	EGCUT_WGS	ss3661952040	Jul 13, 2019 (153)
55	EVA_DECODE	ss3711262928	Jul 13, 2019 (153)
56	ILLUMINA	ss3745238091	Jul 13, 2019 (153)
57	ILLUMINA	ss3772732893	Jul 13, 2019 (153)
58	EVA	ss3828332674	Apr 25, 2020 (154)
59	SGDP_PRJ	ss3858050764	Apr 25, 2020 (154)
60	EVA	ss4017129460	Apr 26, 2021 (155)
61	TOPMED	ss4600618367	Apr 26, 2021 (155)
62	1000G_HIGH_COVERAGE	ss5257789292	Oct 13, 2022 (156)
63	EVA	ss5346457229	Oct 13, 2022 (156)
64	HUGCELL_USP	ss5456736909	Oct 13, 2022 (156)
65	EVA	ss5507371210	Oct 13, 2022 (156)
66	1000G_HIGH_COVERAGE	ss5538109359	Oct 13, 2022 (156)
67	SANFORD_IMAGENETICS	ss5634198229	Oct 13, 2022 (156)
68	EVA	ss5843446476	Oct 13, 2022 (156)
69	EVA	ss5861868797	Oct 13, 2022 (156)
70	EVA	ss5962573922	Oct 13, 2022 (156)
71	1000Genomes	NC_000004.11 - 3242920	Oct 12, 2018 (152)
72	1000Genomes_30x	NC_000004.12 - 3241193	Oct 13, 2022 (156)
73	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 3242920	Oct 12, 2018 (152)
74	Chileans	NC_000004.11 - 3242920	Apr 25, 2020 (154)
75	Genetic variation in the Estonian population	NC_000004.11 - 3242920	Oct 12, 2018 (152)
76	gnomAD - Genomes	NC_000004.12 - 3241193	Apr 26, 2021 (155)
77	Genome of the Netherlands Release 5	NC_000004.11 - 3242920	Apr 25, 2020 (154)
78	HapMap	NC_000004.12 - 3241193	Apr 25, 2020 (154)
79	Qatari	NC_000004.11 - 3242920	Apr 25, 2020 (154)
80	SGDP_PRJ	NC_000004.11 - 3242920	Apr 25, 2020 (154)
81	TopMed	NC_000004.12 - 3241193	Apr 26, 2021 (155)
82	UK 10K study - Twins	NC_000004.11 - 3242920	Oct 12, 2018 (152)
83	ALFA	NC_000004.12 - 3241193	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss116841450, ss197915409, ss480797707, ss484804198, ss1589181505, ss1712646342, ss3643421123	NC_000004.10:3212717:C:T	NC_000004.12:3241192:C:T	(self)
19479462, 10857431, 307082, 7690288, 4770458, 4958799, 10067744, 10857431, ss220699699, ss479709617, ss480813397, ss481737949, ss485193619, ss533214639, ss557261838, ss779167759, ss781049065, ss783042866, ss832300624, ss834632885, ss979685318, ss1071222712, ss1308139853, ss1609262823, ss1652256856, ss1752519562, ss1800830939, ss1922916869, ss2022031980, ss2634072304, ss2634072305, ss2804837793, ss2985906839, ss2994013216, ss3345503812, ss3628886339, ss3632011734, ss3633323543, ss3634042017, ss3634937851, ss3635725224, ss3636636408, ss3637477692, ss3638468255, ss3640645147, ss3661952040, ss3745238091, ss3772732893, ss3828332674, ss3858050764, ss4017129460, ss5346457229, ss5507371210, ss5634198229, ss5843446476, ss5962573922	NC_000004.11:3242919:C:T	NC_000004.12:3241192:C:T	(self)
25635294, 138296600, 2544739, 437995923, 13395489444, ss2259935375, ss3711262928, ss4600618367, ss5257789292, ss5456736909, ss5538109359, ss5861868797	NC_000004.12:3241192:C:T	NC_000004.12:3241192:C:T	(self)
ss459746, ss4254639, ss23250284, ss75145787, ss76614837, ss119351612, ss160630757, ss173609356	NT_006051.18:1764273:C:T	NC_000004.12:3241192: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 rs362302

PMID	Title	Author	Year	Journal
19361997	Five siRNAs targeting three SNPs may provide therapy for three-quarters of Huntington's disease patients.	Pfister EL et al.	2009	Current biology

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

rs362302