Name: rs13101251
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.

rs13101251

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:9587345 (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>A
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.46935 (13263/28258, 14KJPN)
T=0.39314 (6589/16760, 8.3KJPN)
T=0.4600 (2946/6404, 1000G_30x) (+ 9 more)
T=0.3871 (2370/6122, ALFA)
T=0.3029 (1517/5008, 1000G)
A=0.4874 (1428/2930, KOREAN)
A=0.4836 (886/1832, Korea1K)
T=0.170 (170/998, GoNL)
T=0.188 (91/484, SGDP_PRJ)
T=0.176 (38/216, Qatari)
T=0.10 (5/50, Siberian)
T=0.03 (1/40, GENOME_DK)

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	6122	T=0.3871	A=0.6129
European	Sub	5152	T=0.3263	A=0.6737
African	Sub	844	T=0.675	A=0.325
African Others	Sub	42	T=0.74	A=0.26
African American	Sub	802	T=0.672	A=0.328
Asian	Sub	14	T=1.00	A=0.00
East Asian	Sub	10	T=1.0	A=0.0
Other Asian	Sub	4	T=1.0	A=0.0
Latin American 1	Sub	10	T=1.0	A=0.0
Latin American 2	Sub	44	T=1.00	A=0.00
South Asian	Sub	16	T=1.00	A=0.00
Other	Sub	42	T=0.83	A=0.17

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
14KJPN	JAPANESE	Study-wide	28258	T=0.53065	A=0.46935
8.3KJPN	JAPANESE	Study-wide	16760	T=0.39314	A=0.60686
1000Genomes_30x	Global	Study-wide	6404	T=0.4600	A=0.5400
1000Genomes_30x	African	Sub	1786	T=0.5168	A=0.4832
1000Genomes_30x	Europe	Sub	1266	T=0.3325	A=0.6675
1000Genomes_30x	South Asian	Sub	1202	T=0.4983	A=0.5017
1000Genomes_30x	East Asian	Sub	1170	T=0.5214	A=0.4786
1000Genomes_30x	American	Sub	980	T=0.401	A=0.599
Allele Frequency Aggregator	Total	Global	6122	T=0.3871	A=0.6129
Allele Frequency Aggregator	European	Sub	5152	T=0.3263	A=0.6737
Allele Frequency Aggregator	African	Sub	844	T=0.675	A=0.325
Allele Frequency Aggregator	Latin American 2	Sub	44	T=1.00	A=0.00
Allele Frequency Aggregator	Other	Sub	42	T=0.83	A=0.17
Allele Frequency Aggregator	South Asian	Sub	16	T=1.00	A=0.00
Allele Frequency Aggregator	Asian	Sub	14	T=1.00	A=0.00
Allele Frequency Aggregator	Latin American 1	Sub	10	T=1.0	A=0.0
1000Genomes	Global	Study-wide	5008	T=0.3029	A=0.6971
1000Genomes	African	Sub	1322	T=0.4349	A=0.5651
1000Genomes	East Asian	Sub	1008	T=0.3909	A=0.6091
1000Genomes	Europe	Sub	1006	T=0.0537	A=0.9463
1000Genomes	South Asian	Sub	978	T=0.346	A=0.654
1000Genomes	American	Sub	694	T=0.225	A=0.775
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.5126	A=0.4874
Korean Genome Project	KOREAN	Study-wide	1832	T=0.5164	A=0.4836
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.170	A=0.830
SGDP_PRJ	Global	Study-wide	484	T=0.188	A=0.812
Qatari	Global	Study-wide	216	T=0.176	A=0.824
Siberian	Global	Study-wide	50	T=0.10	A=0.90
The Danish reference pan genome	Danish	Study-wide	40	T=0.03	A=0.97

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.9587345T>A
GRCh37.p13 chr 4	NC_000004.11:g.9588969T>A

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=	A
GRCh38.p14 chr 4	NC_000004.12:g.9587345=	NC_000004.12:g.9587345T>A
GRCh37.p13 chr 4	NC_000004.11:g.9588969=	NC_000004.11:g.9588969T>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#.

46 SubSNP, 12 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SSAHASNP	ss22036436	Apr 05, 2004 (121)
2	ABI	ss42388508	Mar 13, 2006 (126)
3	BCMHGSC_JDW	ss92464392	Mar 24, 2008 (129)
4	HUMANGENOME_JCVI	ss98800520	Feb 05, 2009 (130)
5	BGI	ss104039342	Dec 01, 2009 (131)
6	ENSEMBL	ss134605350	Dec 01, 2009 (131)
7	ENSEMBL	ss139435054	Dec 01, 2009 (131)
8	GMI	ss156846333	Dec 01, 2009 (131)
9	BUSHMAN	ss198019815	Jul 04, 2010 (132)
10	BCM-HGSC-SUB	ss206637079	Jul 04, 2010 (132)
11	BL	ss252922774	May 09, 2011 (134)
12	GMI	ss277569542	May 04, 2012 (137)
13	GMI	ss284842992	Apr 25, 2013 (138)
14	1000GENOMES	ss331429270	May 09, 2011 (134)
15	SSMP	ss651064665	Apr 25, 2013 (138)
16	EVA-GONL	ss979751664	Aug 21, 2014 (142)
17	1000GENOMES	ss1308387006	Aug 21, 2014 (142)
18	DDI	ss1429769033	Apr 01, 2015 (144)
19	EVA_GENOME_DK	ss1580409040	Apr 01, 2015 (144)
20	HAMMER_LAB	ss1801002894	Sep 08, 2015 (146)
21	WEILL_CORNELL_DGM	ss1922991788	Feb 12, 2016 (147)
22	GENOMED	ss1969654518	Sep 14, 2016 (149)
23	USC_VALOUEV	ss2150177520	Dec 20, 2016 (150)
24	GRF	ss2705619348	Nov 08, 2017 (151)
25	SWEGEN	ss2994122743	Nov 08, 2017 (151)
26	CSHL	ss3345538274	Nov 08, 2017 (151)
27	URBANLAB	ss3647649064	Oct 12, 2018 (152)
28	EVA	ss3761383412	Jul 13, 2019 (153)
29	PACBIO	ss3784615493	Jul 13, 2019 (153)
30	PACBIO	ss3790086219	Jul 13, 2019 (153)
31	PACBIO	ss3794961200	Jul 13, 2019 (153)
32	KHV_HUMAN_GENOMES	ss3804519446	Jul 13, 2019 (153)
33	EVA	ss3828364407	Apr 25, 2020 (154)
34	SGDP_PRJ	ss3858199250	Apr 25, 2020 (154)
35	KRGDB	ss3904340656	Apr 25, 2020 (154)
36	KOGIC	ss3953512124	Apr 25, 2020 (154)
37	TOMMO_GENOMICS	ss5164156882	Apr 26, 2021 (155)
38	EVA	ss5507381898	Oct 13, 2022 (156)
39	1000G_HIGH_COVERAGE	ss5538425737	Oct 13, 2022 (156)
40	SANFORD_IMAGENETICS	ss5634329123	Oct 13, 2022 (156)
41	TOMMO_GENOMICS	ss5697794502	Oct 13, 2022 (156)
42	YY_MCH	ss5804748968	Oct 13, 2022 (156)
43	EVA	ss5843537893	Oct 13, 2022 (156)
44	EVA	ss5862102955	Oct 13, 2022 (156)
45	EVA	ss5962701061	Oct 13, 2022 (156)
46	EVA	ss5980207110	Oct 13, 2022 (156)
47	1000Genomes	NC_000004.11 - 9588969	Oct 12, 2018 (152)
48	1000Genomes_30x	NC_000004.12 - 9587345	Oct 13, 2022 (156)
49	The Danish reference pan genome	NC_000004.11 - 9588969	Apr 25, 2020 (154)
50	Genome of the Netherlands Release 5	NC_000004.11 - 9588969	Apr 25, 2020 (154)
51	KOREAN population from KRGDB	NC_000004.11 - 9588969	Apr 25, 2020 (154)
52	Korean Genome Project	NC_000004.12 - 9587345	Apr 25, 2020 (154)
53	Qatari	NC_000004.11 - 9588969	Apr 25, 2020 (154)
54	SGDP_PRJ	NC_000004.11 - 9588969	Apr 25, 2020 (154)
55	Siberian	NC_000004.11 - 9588969	Apr 25, 2020 (154)
56	8.3KJPN	NC_000004.11 - 9588969	Apr 26, 2021 (155)
57	14KJPN	NC_000004.12 - 9587345	Oct 13, 2022 (156)
58	ALFA	NC_000004.12 - 9587345	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
ss92464392, ss198019815, ss206637079, ss252922774, ss277569542, ss284842992	NC_000004.10:9198066:T:A	NC_000004.12:9587344:T:A	(self)
19733508, 6573979, 4832935, 11518050, 5033718, 10216230, 2693874, 22126189, ss331429270, ss651064665, ss979751664, ss1308387006, ss1429769033, ss1580409040, ss1801002894, ss1922991788, ss1969654518, ss2150177520, ss2705619348, ss2994122743, ss3345538274, ss3761383412, ss3784615493, ss3790086219, ss3794961200, ss3828364407, ss3858199250, ss3904340656, ss5164156882, ss5507381898, ss5634329123, ss5843537893, ss5962701061, ss5980207110	NC_000004.11:9588968:T:A	NC_000004.12:9587344:T:A	(self)
25951672, 9890125, 31631606, 7509596297, ss3647649064, ss3804519446, ss3953512124, ss5538425737, ss5697794502, ss5804748968, ss5862102955	NC_000004.12:9587344:T:A	NC_000004.12:9587344:T:A	(self)
ss22036436	NT_006316.15:264326:T:A	NC_000004.12:9587344:T:A	(self)
ss42388508, ss98800520, ss104039342, ss134605350, ss139435054, ss156846333	NT_006316.16:770765:T:A	NC_000004.12:9587344:T:A	(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 rs13101251

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

rs13101251