Name: rs13102260
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.

rs13102260

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:3074678 (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: G>A
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.154071 (40781/264690, TOPMED)
A=0.156593 (21483/137190, GnomAD)
A=0.11183 (4655/41626, ALFA) (+ 16 more)
A=0.07539 (2129/28238, 14KJPN)
A=0.07209 (1208/16756, 8.3KJPN)
A=0.1630 (1044/6404, 1000G_30x)
A=0.1581 (792/5008, 1000G)
A=0.1214 (544/4480, Estonian)
A=0.0768 (296/3854, ALSPAC)
A=0.0696 (258/3708, TWINSUK)
A=0.1198 (346/2888, KOREAN)
A=0.1147 (203/1770, Korea1K)
A=0.062 (37/600, NorthernSweden)
A=0.116 (25/216, Qatari)
A=0.094 (20/212, Vietnamese)
G=0.389 (49/126, SGDP_PRJ)
A=0.08 (3/38, GENOME_DK)
G=0.5 (5/10, Siberian)
A=0.5 (5/10, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: HTT : 2KB Upstream Variant
HTT-AS : 2KB Upstream Variant
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: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	41626	G=0.88817	A=0.11183
European	Sub	28268	G=0.91588	A=0.08412
African	Sub	4590	G=0.6959	A=0.3041
African Others	Sub	172	G=0.645	A=0.355
African American	Sub	4418	G=0.6978	A=0.3022
Asian	Sub	148	G=0.926	A=0.074
East Asian	Sub	114	G=0.930	A=0.070
Other Asian	Sub	34	G=0.91	A=0.09
Latin American 1	Sub	542	G=0.876	A=0.124
Latin American 2	Sub	4680	G=0.8972	A=0.1028
South Asian	Sub	144	G=0.951	A=0.049
Other	Sub	3254	G=0.9032	A=0.0968

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	G=0.845929	A=0.154071
gnomAD - Genomes	Global	Study-wide	137190	G=0.843407	A=0.156593
gnomAD - Genomes	European	Sub	74632	G=0.91589	A=0.08411
gnomAD - Genomes	African	Sub	41630	G=0.69123	A=0.30877
gnomAD - Genomes	American	Sub	12970	G=0.90123	A=0.09877
gnomAD - Genomes	Ashkenazi Jewish	Sub	3260	G=0.8525	A=0.1475
gnomAD - Genomes	East Asian	Sub	2616	G=0.8811	A=0.1189
gnomAD - Genomes	Other	Sub	2082	G=0.8660	A=0.1340
Allele Frequency Aggregator	Total	Global	41626	G=0.88817	A=0.11183
Allele Frequency Aggregator	European	Sub	28268	G=0.91588	A=0.08412
Allele Frequency Aggregator	Latin American 2	Sub	4680	G=0.8972	A=0.1028
Allele Frequency Aggregator	African	Sub	4590	G=0.6959	A=0.3041
Allele Frequency Aggregator	Other	Sub	3254	G=0.9032	A=0.0968
Allele Frequency Aggregator	Latin American 1	Sub	542	G=0.876	A=0.124
Allele Frequency Aggregator	Asian	Sub	148	G=0.926	A=0.074
Allele Frequency Aggregator	South Asian	Sub	144	G=0.951	A=0.049
14KJPN	JAPANESE	Study-wide	28238	G=0.92461	A=0.07539
8.3KJPN	JAPANESE	Study-wide	16756	G=0.92791	A=0.07209
1000Genomes_30x	Global	Study-wide	6404	G=0.8370	A=0.1630
1000Genomes_30x	African	Sub	1786	G=0.6288	A=0.3712
1000Genomes_30x	Europe	Sub	1266	G=0.9155	A=0.0845
1000Genomes_30x	South Asian	Sub	1202	G=0.9634	A=0.0366
1000Genomes_30x	East Asian	Sub	1170	G=0.8897	A=0.1103
1000Genomes_30x	American	Sub	980	G=0.897	A=0.103
1000Genomes	Global	Study-wide	5008	G=0.8419	A=0.1581
1000Genomes	African	Sub	1322	G=0.6354	A=0.3646
1000Genomes	East Asian	Sub	1008	G=0.8909	A=0.1091
1000Genomes	Europe	Sub	1006	G=0.9135	A=0.0865
1000Genomes	South Asian	Sub	978	G=0.964	A=0.036
1000Genomes	American	Sub	694	G=0.888	A=0.112
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.8786	A=0.1214
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.9232	A=0.0768
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.9304	A=0.0696
KOREAN population from KRGDB	KOREAN	Study-wide	2888	G=0.8802	A=0.1198
Korean Genome Project	KOREAN	Study-wide	1770	G=0.8853	A=0.1147
Northern Sweden	ACPOP	Study-wide	600	G=0.938	A=0.062
Qatari	Global	Study-wide	216	G=0.884	A=0.116
A Vietnamese Genetic Variation Database	Global	Study-wide	212	G=0.906	A=0.094
SGDP_PRJ	Global	Study-wide	126	G=0.389	A=0.611
The Danish reference pan genome	Danish	Study-wide	38	G=0.92	A=0.08
Siberian	Global	Study-wide	10	G=0.5	A=0.5

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.3074678G>A
GRCh37.p13 chr 4	NC_000004.11:g.3076405G>A
HTT RefSeqGene (LRG_763)	NG_009378.1:g.4998G>A

Gene: HTT, huntingtin (plus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
HTT transcript variant 1	NM_001388492.1:c.	N/A	Upstream Transcript Variant
HTT transcript variant 2	NM_002111.8:c.	N/A	Upstream Transcript Variant

Gene: HTT-AS, HTT antisense RNA (minus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
HTT-AS transcript	NR_045414.1:n.	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	G=	A
GRCh38.p14 chr 4	NC_000004.12:g.3074678=	NC_000004.12:g.3074678G>A
GRCh37.p13 chr 4	NC_000004.11:g.3076405=	NC_000004.11:g.3076405G>A
HTT RefSeqGene (LRG_763)	NG_009378.1:g.4998=	NG_009378.1:g.4998G>A
HTT transcript	NM_002111.7:c.-148=	NM_002111.7:c.-148G>A

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#.

57 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SSAHASNP	ss22040002	Apr 05, 2004 (121)
2	ABI	ss42202588	Mar 15, 2006 (126)
3	ENSEMBL	ss143558621	Dec 01, 2009 (131)
4	ILLUMINA	ss160317184	Dec 01, 2009 (131)
5	BUSHMAN	ss197913585	Jul 04, 2010 (132)
6	1000GENOMES	ss220699171	Jul 14, 2010 (132)
7	1000GENOMES	ss232228875	Jul 14, 2010 (132)
8	1000GENOMES	ss239557163	Jul 15, 2010 (132)
9	PJP	ss293055706	May 09, 2011 (134)
10	ILLUMINA	ss479359763	May 04, 2012 (137)
11	ILLUMINA	ss480485351	Sep 08, 2015 (146)
12	ILLUMINA	ss484801879	May 04, 2012 (137)
13	SSMP	ss651015382	Apr 25, 2013 (138)
14	ILLUMINA	ss780961979	Sep 08, 2015 (146)
15	EVA-GONL	ss979684080	Aug 21, 2014 (142)
16	1000GENOMES	ss1308134890	Aug 21, 2014 (142)
17	EVA_GENOME_DK	ss1580384042	Apr 01, 2015 (144)
18	EVA_DECODE	ss1589180268	Apr 01, 2015 (144)
19	EVA_UK10K_ALSPAC	ss1609260104	Apr 01, 2015 (144)
20	EVA_UK10K_TWINSUK	ss1652254137	Apr 01, 2015 (144)
21	WEILL_CORNELL_DGM	ss1922915834	Feb 12, 2016 (147)
22	ILLUMINA	ss1958651858	Feb 12, 2016 (147)
23	JJLAB	ss2022031338	Sep 14, 2016 (149)
24	USC_VALOUEV	ss2150138204	Dec 20, 2016 (150)
25	ILLUMINA	ss2634072192	Nov 08, 2017 (151)
26	GRF	ss2705572841	Nov 08, 2017 (151)
27	GNOMAD	ss2804823776	Nov 08, 2017 (151)
28	AFFY	ss2985906578	Nov 08, 2017 (151)
29	SWEGEN	ss2994011440	Nov 08, 2017 (151)
30	ILLUMINA	ss3022338289	Nov 08, 2017 (151)
31	ILLUMINA	ss3636636362	Oct 12, 2018 (152)
32	ILLUMINA	ss3642311760	Oct 12, 2018 (152)
33	URBANLAB	ss3647634571	Oct 12, 2018 (152)
34	ILLUMINA	ss3652820824	Oct 12, 2018 (152)
35	EGCUT_WGS	ss3661950072	Jul 13, 2019 (153)
36	EVA_DECODE	ss3711260572	Jul 13, 2019 (153)
37	ACPOP	ss3730787771	Jul 13, 2019 (153)
38	EVA	ss3761299724	Jul 13, 2019 (153)
39	KHV_HUMAN_GENOMES	ss3804437919	Jul 13, 2019 (153)
40	EVA	ss3825652219	Apr 25, 2020 (154)
41	EVA	ss3828332142	Apr 25, 2020 (154)
42	SGDP_PRJ	ss3858048494	Apr 25, 2020 (154)
43	KRGDB	ss3904182287	Apr 25, 2020 (154)
44	KOGIC	ss3953380878	Apr 25, 2020 (154)
45	FSA-LAB	ss3984275996	Apr 26, 2021 (155)
46	TOPMED	ss4600575783	Apr 26, 2021 (155)
47	TOMMO_GENOMICS	ss5163876015	Apr 26, 2021 (155)
48	EVA	ss5237180817	Apr 26, 2021 (155)
49	1000G_HIGH_COVERAGE	ss5257785182	Oct 13, 2022 (156)
50	1000G_HIGH_COVERAGE	ss5538103027	Oct 13, 2022 (156)
51	EVA	ss5624136661	Oct 13, 2022 (156)
52	SANFORD_IMAGENETICS	ss5634196070	Oct 13, 2022 (156)
53	TOMMO_GENOMICS	ss5697432288	Oct 13, 2022 (156)
54	YY_MCH	ss5804687652	Oct 13, 2022 (156)
55	EVA	ss5843444847	Oct 13, 2022 (156)
56	EVA	ss5861863795	Oct 13, 2022 (156)
57	EVA	ss5962571467	Oct 13, 2022 (156)
58	1000Genomes	NC_000004.11 - 3076405	Oct 12, 2018 (152)
59	1000Genomes_30x	NC_000004.12 - 3074678	Oct 13, 2022 (156)
60	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 3076405	Oct 12, 2018 (152)
61	Genetic variation in the Estonian population	NC_000004.11 - 3076405	Oct 12, 2018 (152)
62	The Danish reference pan genome	NC_000004.11 - 3076405	Apr 25, 2020 (154)
63	gnomAD - Genomes	NC_000004.12 - 3074678	Apr 26, 2021 (155)
64	KOREAN population from KRGDB	NC_000004.11 - 3076405	Apr 25, 2020 (154)
65	Korean Genome Project	NC_000004.12 - 3074678	Apr 25, 2020 (154)
66	Northern Sweden	NC_000004.11 - 3076405	Jul 13, 2019 (153)
67	Qatari	NC_000004.11 - 3076405	Apr 25, 2020 (154)
68	SGDP_PRJ	NC_000004.11 - 3076405	Apr 25, 2020 (154)
69	Siberian	NC_000004.11 - 3076405	Apr 25, 2020 (154)
70	8.3KJPN	NC_000004.11 - 3076405	Apr 26, 2021 (155)
71	14KJPN	NC_000004.12 - 3074678	Oct 13, 2022 (156)
72	TopMed	NC_000004.12 - 3074678	Apr 26, 2021 (155)
73	UK 10K study - Twins	NC_000004.11 - 3076405	Oct 12, 2018 (152)
74	A Vietnamese Genetic Variation Database	NC_000004.11 - 3076405	Jul 13, 2019 (153)
75	ALFA	NC_000004.12 - 3074678	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
ss197913585, ss293055706, ss484801879, ss1589180268	NC_000004.10:3046202:G:A	NC_000004.12:3074677:G:A	(self)
19474360, 10854472, 7688320, 6548981, 11359681, 4072636, 4957764, 10065474, 2654558, 21845322, 10854472, 2372000, ss220699171, ss232228875, ss239557163, ss479359763, ss480485351, ss651015382, ss780961979, ss979684080, ss1308134890, ss1580384042, ss1609260104, ss1652254137, ss1922915834, ss1958651858, ss2022031338, ss2150138204, ss2634072192, ss2705572841, ss2804823776, ss2985906578, ss2994011440, ss3022338289, ss3636636362, ss3642311760, ss3652820824, ss3661950072, ss3730787771, ss3761299724, ss3825652219, ss3828332142, ss3858048494, ss3904182287, ss3984275996, ss5163876015, ss5624136661, ss5634196070, ss5843444847, ss5962571467	NC_000004.11:3076404:G:A	NC_000004.12:3074677:G:A	(self)
25628962, 138261088, 9758879, 31269392, 437953339, 696531744, ss3647634571, ss3711260572, ss3804437919, ss3953380878, ss4600575783, ss5237180817, ss5257785182, ss5538103027, ss5697432288, ss5804687652, ss5861863795	NC_000004.12:3074677:G:A	NC_000004.12:3074677:G:A	(self)
ss42202588, ss143558621, ss160317184	NT_006051.18:1597758:G:A	NC_000004.12:3074677:G:A	(self)
ss22040002	NT_006081.16:462981:G:A	NC_000004.12:3074677:G:A	(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 rs13102260

PMID	Title	Author	Year	Journal
25938884	A SNP in the HTT promoter alters NF-κB binding and is a bidirectional genetic modifier of Huntington disease.	Bečanović K et al.	2015	Nature neuroscience
33147747	Pathogenic Single Nucleotide Polymorphisms on Autophagy-Related Genes.	Tamargo-Gómez I et al.	2020	International journal of molecular sciences

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

rs13102260