Name: rs1002681
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.

rs1002681

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:163928451 (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=0.490736 (129893/264690, TOPMED)
T=0.491351 (68799/140020, GnomAD)
T=0.44471 (30324/68188, ALFA) (+ 20 more)
T=0.48903 (13818/28256, 14KJPN)
T=0.48890 (8194/16760, 8.3KJPN)
C=0.4828 (3092/6404, 1000G_30x)
C=0.4940 (2474/5008, 1000G)
T=0.4810 (2155/4480, Estonian)
T=0.4248 (1637/3854, ALSPAC)
T=0.4167 (1545/3708, TWINSUK)
T=0.4164 (1220/2930, KOREAN)
T=0.4712 (982/2084, HGDP_Stanford)
C=0.4884 (924/1892, HapMap)
T=0.4203 (770/1832, Korea1K)
T=0.432 (431/998, GoNL)
T=0.398 (239/600, NorthernSweden)
C=0.357 (142/398, SGDP_PRJ)
T=0.319 (69/216, Qatari)
T=0.304 (65/214, Vietnamese)
T=0.29 (20/70, Ancient Sardinia)
C=0.27 (13/48, Siberian)
C=0.50 (20/40, GENOME_DK)
T=0.50 (20/40, 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	68188	C=0.55529	T=0.44471
European	Sub	55584	C=0.57803	T=0.42197
African	Sub	4526	C=0.3588	T=0.6412
African Others	Sub	170	C=0.294	T=0.706
African American	Sub	4356	C=0.3613	T=0.6387
Asian	Sub	190	C=0.547	T=0.453
East Asian	Sub	148	C=0.534	T=0.466
Other Asian	Sub	42	C=0.60	T=0.40
Latin American 1	Sub	254	C=0.531	T=0.469
Latin American 2	Sub	1232	C=0.5065	T=0.4935
South Asian	Sub	4956	C=0.4974	T=0.5026
Other	Sub	1446	C=0.5415	T=0.4585

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=0.509264	T=0.490736
gnomAD - Genomes	Global	Study-wide	140020	C=0.508649	T=0.491351
gnomAD - Genomes	European	Sub	75852	C=0.57694	T=0.42306
gnomAD - Genomes	African	Sub	41948	C=0.36066	T=0.63934
gnomAD - Genomes	American	Sub	13640	C=0.52067	T=0.47933
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	C=0.6216	T=0.3784
gnomAD - Genomes	East Asian	Sub	3108	C=0.6396	T=0.3604
gnomAD - Genomes	Other	Sub	2150	C=0.5465	T=0.4535
Allele Frequency Aggregator	Total	Global	68188	C=0.55529	T=0.44471
Allele Frequency Aggregator	European	Sub	55584	C=0.57803	T=0.42197
Allele Frequency Aggregator	South Asian	Sub	4956	C=0.4974	T=0.5026
Allele Frequency Aggregator	African	Sub	4526	C=0.3588	T=0.6412
Allele Frequency Aggregator	Other	Sub	1446	C=0.5415	T=0.4585
Allele Frequency Aggregator	Latin American 2	Sub	1232	C=0.5065	T=0.4935
Allele Frequency Aggregator	Latin American 1	Sub	254	C=0.531	T=0.469
Allele Frequency Aggregator	Asian	Sub	190	C=0.547	T=0.453
14KJPN	JAPANESE	Study-wide	28256	C=0.51097	T=0.48903
8.3KJPN	JAPANESE	Study-wide	16760	C=0.51110	T=0.48890
1000Genomes_30x	Global	Study-wide	6404	C=0.4828	T=0.5172
1000Genomes_30x	African	Sub	1786	C=0.3040	T=0.6960
1000Genomes_30x	Europe	Sub	1266	C=0.5916	T=0.4084
1000Genomes_30x	South Asian	Sub	1202	C=0.4942	T=0.5058
1000Genomes_30x	East Asian	Sub	1170	C=0.6265	T=0.3735
1000Genomes_30x	American	Sub	980	C=0.483	T=0.517
1000Genomes	Global	Study-wide	5008	C=0.4940	T=0.5060
1000Genomes	African	Sub	1322	C=0.3048	T=0.6952
1000Genomes	East Asian	Sub	1008	C=0.6310	T=0.3690
1000Genomes	Europe	Sub	1006	C=0.6054	T=0.3946
1000Genomes	South Asian	Sub	978	C=0.494	T=0.506
1000Genomes	American	Sub	694	C=0.494	T=0.506
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.5190	T=0.4810
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.5752	T=0.4248
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.5833	T=0.4167
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.5836	T=0.4164
HGDP-CEPH-db Supplement 1	Global	Study-wide	2084	C=0.5288	T=0.4712
HGDP-CEPH-db Supplement 1	Est_Asia	Sub	470	C=0.628	T=0.372
HGDP-CEPH-db Supplement 1	Central_South_Asia	Sub	414	C=0.466	T=0.534
HGDP-CEPH-db Supplement 1	Middle_Est	Sub	350	C=0.531	T=0.469
HGDP-CEPH-db Supplement 1	Europe	Sub	320	C=0.641	T=0.359
HGDP-CEPH-db Supplement 1	Africa	Sub	242	C=0.364	T=0.636
HGDP-CEPH-db Supplement 1	America	Sub	216	C=0.315	T=0.685
HGDP-CEPH-db Supplement 1	Oceania	Sub	72	C=0.93	T=0.07
HapMap	Global	Study-wide	1892	C=0.4884	T=0.5116
HapMap	American	Sub	770	C=0.551	T=0.449
HapMap	African	Sub	692	C=0.327	T=0.673
HapMap	Asian	Sub	254	C=0.626	T=0.374
HapMap	Europe	Sub	176	C=0.653	T=0.347
Korean Genome Project	KOREAN	Study-wide	1832	C=0.5797	T=0.4203
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.568	T=0.432
Northern Sweden	ACPOP	Study-wide	600	C=0.602	T=0.398
SGDP_PRJ	Global	Study-wide	398	C=0.357	T=0.643
Qatari	Global	Study-wide	216	C=0.681	T=0.319
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.696	T=0.304
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	70	C=0.71	T=0.29
Siberian	Global	Study-wide	48	C=0.27	T=0.73
The Danish reference pan genome	Danish	Study-wide	40	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 1	NC_000001.11:g.163928451C>T
GRCh37.p13 chr 1	NC_000001.10:g.163897688C>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 1	NC_000001.11:g.163928451=	NC_000001.11:g.163928451C>T
GRCh37.p13 chr 1	NC_000001.10:g.163897688=	NC_000001.10:g.163897688C>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#.

98 SubSNP, 22 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss1463528	Oct 05, 2000 (86)
2	TSC-CSHL	ss5158867	Oct 08, 2002 (108)
3	WI_SSAHASNP	ss6410583	Feb 20, 2003 (111)
4	WI_SSAHASNP	ss11402293	Jul 11, 2003 (116)
5	SSAHASNP	ss20484533	Apr 05, 2004 (121)
6	ILLUMINA	ss65714025	Oct 15, 2006 (127)
7	ILLUMINA	ss66696644	Nov 30, 2006 (127)
8	ILLUMINA	ss66865156	Nov 30, 2006 (127)
9	ILLUMINA	ss66935712	Nov 30, 2006 (127)
10	ILLUMINA	ss70356579	May 17, 2007 (127)
11	ILLUMINA	ss70460530	May 25, 2008 (130)
12	ILLUMINA	ss70981224	May 17, 2007 (127)
13	ILLUMINA	ss75659167	Dec 07, 2007 (129)
14	HGSV	ss78084379	Dec 07, 2007 (129)
15	KRIBB_YJKIM	ss83651626	Dec 15, 2007 (130)
16	HUMANGENOME_JCVI	ss99256332	Feb 05, 2009 (130)
17	BGI	ss102791830	Dec 01, 2009 (131)
18	1000GENOMES	ss108650473	Jan 23, 2009 (130)
19	1000GENOMES	ss111255755	Jan 25, 2009 (130)
20	ILLUMINA	ss121254420	Dec 01, 2009 (131)
21	ENSEMBL	ss131703203	Dec 01, 2009 (131)
22	ILLUMINA	ss152545764	Dec 01, 2009 (131)
23	ILLUMINA	ss159104448	Dec 01, 2009 (131)
24	COMPLETE_GENOMICS	ss164273933	Jul 04, 2010 (132)
25	COMPLETE_GENOMICS	ss165334313	Jul 04, 2010 (132)
26	ILLUMINA	ss169218302	Jul 04, 2010 (132)
27	ILLUMINA	ss169532732	Jul 04, 2010 (132)
28	BUSHMAN	ss199168299	Jul 04, 2010 (132)
29	BCM-HGSC-SUB	ss205306736	Jul 04, 2010 (132)
30	1000GENOMES	ss218684991	Jul 14, 2010 (132)
31	1000GENOMES	ss230757200	Jul 14, 2010 (132)
32	1000GENOMES	ss238400058	Jul 15, 2010 (132)
33	GMI	ss276077936	May 04, 2012 (137)
34	GMI	ss284164557	Apr 25, 2013 (138)
35	PJP	ss290650801	May 09, 2011 (134)
36	ILLUMINA	ss536567002	Sep 08, 2015 (146)
37	TISHKOFF	ss554781105	Apr 25, 2013 (138)
38	SSMP	ss648458936	Apr 25, 2013 (138)
39	ILLUMINA	ss825326310	Apr 01, 2015 (144)
40	ILLUMINA	ss832617241	Jul 12, 2019 (153)
41	EVA-GONL	ss975751464	Aug 21, 2014 (142)
42	JMKIDD_LAB	ss1068318472	Aug 21, 2014 (142)
43	1000GENOMES	ss1293186789	Aug 21, 2014 (142)
44	DDI	ss1425999326	Apr 01, 2015 (144)
45	EVA_GENOME_DK	ss1574438054	Apr 01, 2015 (144)
46	EVA_DECODE	ss1585135144	Apr 01, 2015 (144)
47	EVA_UK10K_ALSPAC	ss1601352066	Apr 01, 2015 (144)
48	EVA_UK10K_TWINSUK	ss1644346099	Apr 01, 2015 (144)
49	EVA_SVP	ss1712376380	Apr 01, 2015 (144)
50	HAMMER_LAB	ss1795182611	Sep 08, 2015 (146)
51	WEILL_CORNELL_DGM	ss1918987738	Feb 12, 2016 (147)
52	GENOMED	ss1966882945	Jul 19, 2016 (147)
53	JJLAB	ss2020008568	Sep 14, 2016 (149)
54	USC_VALOUEV	ss2148035250	Dec 20, 2016 (150)
55	HUMAN_LONGEVITY	ss2167060308	Dec 20, 2016 (150)
56	SYSTEMSBIOZJU	ss2624513369	Nov 08, 2017 (151)
57	GRF	ss2698011894	Nov 08, 2017 (151)
58	GNOMAD	ss2762060955	Nov 08, 2017 (151)
59	SWEGEN	ss2987860148	Nov 08, 2017 (151)
60	BIOINF_KMB_FNS_UNIBA	ss3023761718	Nov 08, 2017 (151)
61	CSHL	ss3343741295	Nov 08, 2017 (151)
62	ILLUMINA	ss3626226234	Oct 11, 2018 (152)
63	ILLUMINA	ss3637791930	Oct 11, 2018 (152)
64	ILLUMINA	ss3638912470	Oct 11, 2018 (152)
65	ILLUMINA	ss3639454514	Oct 11, 2018 (152)
66	ILLUMINA	ss3642800772	Oct 11, 2018 (152)
67	URBANLAB	ss3646806015	Oct 11, 2018 (152)
68	EGCUT_WGS	ss3655799940	Jul 12, 2019 (153)
69	EVA_DECODE	ss3687911332	Jul 12, 2019 (153)
70	ACPOP	ss3727543013	Jul 12, 2019 (153)
71	EVA	ss3746887985	Jul 12, 2019 (153)
72	PACBIO	ss3783585326	Jul 12, 2019 (153)
73	PACBIO	ss3789213737	Jul 12, 2019 (153)
74	PACBIO	ss3794085757	Jul 12, 2019 (153)
75	KHV_HUMAN_GENOMES	ss3799888378	Jul 12, 2019 (153)
76	EVA	ss3826458882	Apr 25, 2020 (154)
77	EVA	ss3836624510	Apr 25, 2020 (154)
78	EVA	ss3842034189	Apr 25, 2020 (154)
79	HGDP	ss3847351741	Apr 25, 2020 (154)
80	SGDP_PRJ	ss3850141200	Apr 25, 2020 (154)
81	KRGDB	ss3895370060	Apr 25, 2020 (154)
82	KOGIC	ss3945786761	Apr 25, 2020 (154)
83	EVA	ss3984829819	Apr 25, 2021 (155)
84	EVA	ss4016942019	Apr 25, 2021 (155)
85	TOPMED	ss4470593365	Apr 25, 2021 (155)
86	TOMMO_GENOMICS	ss5146784891	Apr 25, 2021 (155)
87	1000G_HIGH_COVERAGE	ss5244519790	Oct 12, 2022 (156)
88	EVA	ss5322461995	Oct 12, 2022 (156)
89	HUGCELL_USP	ss5445082077	Oct 12, 2022 (156)
90	EVA	ss5506051098	Oct 12, 2022 (156)
91	1000G_HIGH_COVERAGE	ss5517961156	Oct 12, 2022 (156)
92	SANFORD_IMAGENETICS	ss5626720043	Oct 12, 2022 (156)
93	TOMMO_GENOMICS	ss5674071303	Oct 12, 2022 (156)
94	YY_MCH	ss5801317874	Oct 12, 2022 (156)
95	EVA	ss5832755584	Oct 12, 2022 (156)
96	EVA	ss5849135452	Oct 12, 2022 (156)
97	EVA	ss5910502557	Oct 12, 2022 (156)
98	EVA	ss5938518022	Oct 12, 2022 (156)
99	1000Genomes	NC_000001.10 - 163897688	Oct 11, 2018 (152)
100	1000Genomes_30x	NC_000001.11 - 163928451	Oct 12, 2022 (156)
101	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 163897688	Oct 11, 2018 (152)
102	Genetic variation in the Estonian population	NC_000001.10 - 163897688	Oct 11, 2018 (152)
103	The Danish reference pan genome	NC_000001.10 - 163897688	Apr 25, 2020 (154)
104	gnomAD - Genomes	NC_000001.11 - 163928451	Apr 25, 2021 (155)
105	Genome of the Netherlands Release 5	NC_000001.10 - 163897688	Apr 25, 2020 (154)
106	HGDP-CEPH-db Supplement 1	NC_000001.9 - 162164312	Apr 25, 2020 (154)
107	HapMap	NC_000001.11 - 163928451	Apr 25, 2020 (154)
108	KOREAN population from KRGDB	NC_000001.10 - 163897688	Apr 25, 2020 (154)
109	Korean Genome Project	NC_000001.11 - 163928451	Apr 25, 2020 (154)
110	Northern Sweden	NC_000001.10 - 163897688	Jul 12, 2019 (153)
111	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000001.10 - 163897688	Apr 25, 2021 (155)
112	Qatari	NC_000001.10 - 163897688	Apr 25, 2020 (154)
113	SGDP_PRJ	NC_000001.10 - 163897688	Apr 25, 2020 (154)
114	Siberian	NC_000001.10 - 163897688	Apr 25, 2020 (154)
115	8.3KJPN	NC_000001.10 - 163897688	Apr 25, 2021 (155)
116	14KJPN	NC_000001.11 - 163928451	Oct 12, 2022 (156)
117	TopMed	NC_000001.11 - 163928451	Apr 25, 2021 (155)
118	UK 10K study - Twins	NC_000001.10 - 163897688	Oct 11, 2018 (152)
119	A Vietnamese Genetic Variation Database	NC_000001.10 - 163897688	Jul 12, 2019 (153)
120	ALFA	NC_000001.11 - 163928451	Apr 25, 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)
rs59368403	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss78084379, ss3638912470, ss3639454514	NC_000001.8:160629345:C:T	NC_000001.11:163928450:C:T	(self)
29633, ss108650473, ss111255755, ss164273933, ss165334313, ss199168299, ss205306736, ss276077936, ss284164557, ss290650801, ss825326310, ss1585135144, ss1712376380, ss3642800772, ss3847351741	NC_000001.9:162164311:C:T	NC_000001.11:163928450:C:T	(self)
3987486, 2172517, 1538188, 1735286, 944654, 2547454, 827878, 55746, 1029668, 2158180, 551604, 4754198, 2172517, 466374, ss218684991, ss230757200, ss238400058, ss536567002, ss554781105, ss648458936, ss832617241, ss975751464, ss1068318472, ss1293186789, ss1425999326, ss1574438054, ss1601352066, ss1644346099, ss1795182611, ss1918987738, ss1966882945, ss2020008568, ss2148035250, ss2624513369, ss2698011894, ss2762060955, ss2987860148, ss3343741295, ss3626226234, ss3637791930, ss3655799940, ss3727543013, ss3746887985, ss3783585326, ss3789213737, ss3794085757, ss3826458882, ss3836624510, ss3850141200, ss3895370060, ss3984829819, ss4016942019, ss5146784891, ss5322461995, ss5506051098, ss5626720043, ss5832755584, ss5938518022	NC_000001.10:163897687:C:T	NC_000001.11:163928450:C:T	(self)
5487091, 28942380, 190568, 2164762, 7908407, 34199700, 1711045912, ss2167060308, ss3023761718, ss3646806015, ss3687911332, ss3799888378, ss3842034189, ss3945786761, ss4470593365, ss5244519790, ss5445082077, ss5517961156, ss5674071303, ss5801317874, ss5849135452, ss5910502557	NC_000001.11:163928450:C:T	NC_000001.11:163928450:C:T	(self)
ss1463528, ss5158867, ss6410583, ss65714025, ss66696644, ss66865156, ss66935712, ss70356579, ss70460530, ss70981224, ss75659167, ss83651626, ss99256332, ss102791830, ss121254420, ss131703203, ss152545764, ss159104448, ss169218302, ss169532732	NT_004487.19:15386329:C:T	NC_000001.11:163928450:C:T	(self)
ss11402293	NT_004668.15:10268246:C:T	NC_000001.11:163928450:C:T	(self)
ss20484533	NT_004668.16:2403159:C:T	NC_000001.11:163928450: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 rs1002681

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs1002681