Name: rs2025993
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.

rs2025993

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:157786218 (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 / T>C / T>G
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.494061 (130773/264690, TOPMED)
A=0.491204 (68575/139606, GnomAD)
T=0.14785 (4178/28258, 14KJPN) (+ 14 more)
A=0.45643 (8622/18890, ALFA)
T=0.14976 (2510/16760, 8.3KJPN)
T=0.3982 (2550/6404, 1000G_30x)
T=0.3932 (1969/5008, 1000G)
A=0.4529 (2029/4480, Estonian)
A=0.4318 (1664/3854, ALSPAC)
A=0.4177 (1549/3708, TWINSUK)
T=0.1188 (348/2930, KOREAN)
A=0.136 (136/998, GoNL)
A=0.385 (231/600, NorthernSweden)
T=0.208 (101/486, SGDP_PRJ)
T=0.495 (107/216, Qatari)
T=0.33 (16/48, Siberian)
T=0.47 (19/40, 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	18890	T=0.54357	A=0.45643
European	Sub	14286	T=0.57553	A=0.42447
African	Sub	2946	T=0.4515	A=0.5485
African Others	Sub	114	T=0.360	A=0.640
African American	Sub	2832	T=0.4552	A=0.5448
Asian	Sub	112	T=0.125	A=0.875
East Asian	Sub	86	T=0.14	A=0.86
Other Asian	Sub	26	T=0.08	A=0.92
Latin American 1	Sub	146	T=0.514	A=0.486
Latin American 2	Sub	610	T=0.372	A=0.628
South Asian	Sub	98	T=0.38	A=0.62
Other	Sub	692	T=0.525	A=0.475

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	T=0.494061	A=0.505939
gnomAD - Genomes	Global	Study-wide	139606	T=0.508796	A=0.491204
gnomAD - Genomes	European	Sub	75658	T=0.57185	A=0.42815
gnomAD - Genomes	African	Sub	41782	T=0.44871	A=0.55129
gnomAD - Genomes	American	Sub	13594	T=0.43402	A=0.56598
gnomAD - Genomes	Ashkenazi Jewish	Sub	3316	T=0.5274	A=0.4726
gnomAD - Genomes	East Asian	Sub	3118	T=0.1074	A=0.8926
gnomAD - Genomes	Other	Sub	2138	T=0.4836	A=0.5164
14KJPN	JAPANESE	Study-wide	28258	T=0.14785	A=0.85215
Allele Frequency Aggregator	Total	Global	18890	T=0.54357	A=0.45643
Allele Frequency Aggregator	European	Sub	14286	T=0.57553	A=0.42447
Allele Frequency Aggregator	African	Sub	2946	T=0.4515	A=0.5485
Allele Frequency Aggregator	Other	Sub	692	T=0.525	A=0.475
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.372	A=0.628
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.514	A=0.486
Allele Frequency Aggregator	Asian	Sub	112	T=0.125	A=0.875
Allele Frequency Aggregator	South Asian	Sub	98	T=0.38	A=0.62
8.3KJPN	JAPANESE	Study-wide	16760	T=0.14976	A=0.85024
1000Genomes_30x	Global	Study-wide	6404	T=0.3982	A=0.6018
1000Genomes_30x	African	Sub	1786	T=0.4479	A=0.5521
1000Genomes_30x	Europe	Sub	1266	T=0.5821	A=0.4179
1000Genomes_30x	South Asian	Sub	1202	T=0.3810	A=0.6190
1000Genomes_30x	East Asian	Sub	1170	T=0.1171	A=0.8829
1000Genomes_30x	American	Sub	980	T=0.427	A=0.573
1000Genomes	Global	Study-wide	5008	T=0.3932	A=0.6068
1000Genomes	African	Sub	1322	T=0.4380	A=0.5620
1000Genomes	East Asian	Sub	1008	T=0.1230	A=0.8770
1000Genomes	Europe	Sub	1006	T=0.5855	A=0.4145
1000Genomes	South Asian	Sub	978	T=0.388	A=0.612
1000Genomes	American	Sub	694	T=0.429	A=0.571
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.5471	A=0.4529
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.5682	A=0.4318
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.5823	A=0.4177
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.1188	A=0.8812, C=0.0000, G=0.0000
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.864	A=0.136
Northern Sweden	ACPOP	Study-wide	600	T=0.615	A=0.385
SGDP_PRJ	Global	Study-wide	486	T=0.208	A=0.792
Qatari	Global	Study-wide	216	T=0.495	A=0.505
Siberian	Global	Study-wide	48	T=0.33	A=0.67
The Danish reference pan genome	Danish	Study-wide	40	T=0.47	A=0.53

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 6	NC_000006.12:g.157786218T>A
GRCh38.p14 chr 6	NC_000006.12:g.157786218T>C
GRCh38.p14 chr 6	NC_000006.12:g.157786218T>G
GRCh37.p13 chr 6	NC_000006.11:g.158207250T>A
GRCh37.p13 chr 6	NC_000006.11:g.158207250T>C
GRCh37.p13 chr 6	NC_000006.11:g.158207250T>G

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	C	G
GRCh38.p14 chr 6	NC_000006.12:g.157786218=	NC_000006.12:g.157786218T>A	NC_000006.12:g.157786218T>C	NC_000006.12:g.157786218T>G
GRCh37.p13 chr 6	NC_000006.11:g.158207250=	NC_000006.11:g.158207250T>A	NC_000006.11:g.158207250T>C	NC_000006.11:g.158207250T>G
SNX9 transcript variant X1	XM_005267015.1:c.-10+6351=	XM_005267015.1:c.-10+6351T>A	XM_005267015.1:c.-10+6351T>C	XM_005267015.1:c.-10+6351T>G

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#.

60 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss2934418	Apr 12, 2001 (94)
2	SC_JCM	ss3971954	Sep 28, 2001 (100)
3	SC_JCM	ss4220364	Nov 05, 2001 (101)
4	SC_SNP	ss12790766	Dec 05, 2003 (119)
5	ABI	ss42710582	Mar 15, 2006 (126)
6	1000GENOMES	ss111187116	Jan 25, 2009 (130)
7	COMPLETE_GENOMICS	ss162953633	Jul 04, 2010 (132)
8	COMPLETE_GENOMICS	ss165046546	Jul 04, 2010 (132)
9	COMPLETE_GENOMICS	ss167430038	Jul 04, 2010 (132)
10	BUSHMAN	ss202654282	Jul 04, 2010 (132)
11	1000GENOMES	ss211954830	Jul 14, 2010 (132)
12	1000GENOMES	ss222783915	Jul 14, 2010 (132)
13	1000GENOMES	ss233759708	Jul 15, 2010 (132)
14	1000GENOMES	ss240759327	Jul 15, 2010 (132)
15	BL	ss254778974	May 09, 2011 (134)
16	GMI	ss279097299	May 04, 2012 (137)
17	PJP	ss293770811	May 09, 2011 (134)
18	SSMP	ss653998153	Apr 25, 2013 (138)
19	EVA-GONL	ss983708994	Aug 21, 2014 (142)
20	JMKIDD_LAB	ss1074191671	Aug 21, 2014 (142)
21	1000GENOMES	ss1323070310	Aug 21, 2014 (142)
22	DDI	ss1430953571	Apr 01, 2015 (144)
23	EVA_GENOME_DK	ss1581976049	Apr 01, 2015 (144)
24	EVA_UK10K_ALSPAC	ss1617127853	Apr 01, 2015 (144)
25	EVA_UK10K_TWINSUK	ss1660121886	Apr 01, 2015 (144)
26	HAMMER_LAB	ss1804761557	Sep 08, 2015 (146)
27	WEILL_CORNELL_DGM	ss1926951606	Feb 12, 2016 (147)
28	JJLAB	ss2024141487	Sep 14, 2016 (149)
29	USC_VALOUEV	ss2152333782	Dec 20, 2016 (150)
30	HUMAN_LONGEVITY	ss2290050765	Dec 20, 2016 (150)
31	SYSTEMSBIOZJU	ss2626560642	Nov 08, 2017 (151)
32	GRF	ss2707972113	Nov 08, 2017 (151)
33	GNOMAD	ss2847374445	Nov 08, 2017 (151)
34	SWEGEN	ss3000266974	Nov 08, 2017 (151)
35	BIOINF_KMB_FNS_UNIBA	ss3025860928	Nov 08, 2017 (151)
36	CSHL	ss3347319258	Nov 08, 2017 (151)
37	ILLUMINA	ss3625917440	Oct 12, 2018 (152)
38	EGCUT_WGS	ss3668206044	Jul 13, 2019 (153)
39	EVA_DECODE	ss3718669290	Jul 13, 2019 (153)
40	ACPOP	ss3734158128	Jul 13, 2019 (153)
41	EVA	ss3765915194	Jul 13, 2019 (153)
42	KHV_HUMAN_GENOMES	ss3809077877	Jul 13, 2019 (153)
43	EVA	ss3830293418	Apr 26, 2020 (154)
44	EVA	ss3838630992	Apr 26, 2020 (154)
45	EVA	ss3844080955	Apr 26, 2020 (154)
46	SGDP_PRJ	ss3866130914	Apr 26, 2020 (154)
47	KRGDB	ss3913117026	Apr 26, 2020 (154)
48	TOPMED	ss4728671361	Apr 26, 2021 (155)
49	TOMMO_GENOMICS	ss5180819218	Apr 26, 2021 (155)
50	1000G_HIGH_COVERAGE	ss5271051266	Oct 13, 2022 (156)
51	HUGCELL_USP	ss5468433139	Oct 13, 2022 (156)
52	1000G_HIGH_COVERAGE	ss5558341667	Oct 13, 2022 (156)
53	SANFORD_IMAGENETICS	ss5641894619	Oct 13, 2022 (156)
54	TOMMO_GENOMICS	ss5719957615	Oct 13, 2022 (156)
55	YY_MCH	ss5808131055	Oct 13, 2022 (156)
56	EVA	ss5843262843	Oct 13, 2022 (156)
57	EVA	ss5855666021	Oct 13, 2022 (156)
58	EVA	ss5886763577	Oct 13, 2022 (156)
59	EVA	ss5970920284	Oct 13, 2022 (156)
60	EVA	ss5970920285	Oct 13, 2022 (156)
61	1000Genomes	NC_000006.11 - 158207250	Oct 12, 2018 (152)
62	1000Genomes_30x	NC_000006.12 - 157786218	Oct 13, 2022 (156)
63	The Avon Longitudinal Study of Parents and Children	NC_000006.11 - 158207250	Oct 12, 2018 (152)
64	Genetic variation in the Estonian population	NC_000006.11 - 158207250	Oct 12, 2018 (152)
65	The Danish reference pan genome	NC_000006.11 - 158207250	Apr 26, 2020 (154)
66	gnomAD - Genomes	NC_000006.12 - 157786218	Apr 26, 2021 (155)
67	Genome of the Netherlands Release 5	NC_000006.11 - 158207250	Apr 26, 2020 (154)
68	KOREAN population from KRGDB	NC_000006.11 - 158207250	Apr 26, 2020 (154)
69	Northern Sweden	NC_000006.11 - 158207250	Jul 13, 2019 (153)
70	Qatari	NC_000006.11 - 158207250	Apr 26, 2020 (154)
71	SGDP_PRJ	NC_000006.11 - 158207250	Apr 26, 2020 (154)
72	Siberian	NC_000006.11 - 158207250	Apr 26, 2020 (154)
73	8.3KJPN	NC_000006.11 - 158207250	Apr 26, 2021 (155)
74	14KJPN	NC_000006.12 - 157786218	Oct 13, 2022 (156)
75	TopMed	NC_000006.12 - 157786218	Apr 26, 2021 (155)
76	UK 10K study - Twins	NC_000006.11 - 158207250	Oct 12, 2018 (152)
77	ALFA	NC_000006.12 - 157786218	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
ss111187116, ss162953633, ss165046546, ss167430038, ss202654282, ss211954830, ss254778974, ss279097299, ss293770811	NC_000006.10:158127237:T:A	NC_000006.12:157786217:T:A	(self)
34969636, 19501709, 13944292, 8140988, 8678960, 20294420, 7442993, 8993536, 18147894, 4850136, 38788525, 19501709, ss222783915, ss233759708, ss240759327, ss653998153, ss983708994, ss1074191671, ss1323070310, ss1430953571, ss1581976049, ss1617127853, ss1660121886, ss1804761557, ss1926951606, ss2024141487, ss2152333782, ss2626560642, ss2707972113, ss2847374445, ss3000266974, ss3347319258, ss3625917440, ss3668206044, ss3734158128, ss3765915194, ss3830293418, ss3838630992, ss3866130914, ss3913117026, ss5180819218, ss5641894619, ss5843262843, ss5970920284, ss5970920285	NC_000006.11:158207249:T:A	NC_000006.12:157786217:T:A	(self)
45867602, 246868183, 53794719, 566048919, 15519422037, ss2290050765, ss3025860928, ss3718669290, ss3809077877, ss3844080955, ss4728671361, ss5271051266, ss5468433139, ss5558341667, ss5719957615, ss5808131055, ss5855666021, ss5886763577	NC_000006.12:157786217:T:A	NC_000006.12:157786217:T:A	(self)
ss2934418, ss3971954, ss4220364, ss12790766, ss42710582	NT_025741.15:62376706:T:A	NC_000006.12:157786217:T:A	(self)
20294420, ss3913117026	NC_000006.11:158207249:T:C	NC_000006.12:157786217:T:C	(self)
20294420, ss3913117026	NC_000006.11:158207249:T:G	NC_000006.12:157786217:T:G	(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 rs2025993

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

rs2025993