Name: rs10164009
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.

rs10164009

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr18:2461961 (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>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.046156 (12217/264690, TOPMED)
C=0.068271 (14216/208228, ALFA)
C=0.050169 (7035/140226, GnomAD) (+ 15 more)
C=0.0212 (136/6404, 1000G_30x)
C=0.0214 (107/5008, 1000G)
C=0.0799 (358/4480, Estonian)
C=0.0708 (273/3854, ALSPAC)
C=0.0736 (273/3708, TWINSUK)
C=0.0003 (1/2922, KOREAN)
C=0.0259 (54/2084, HGDP_Stanford)
C=0.0361 (41/1136, Daghestan)
C=0.069 (69/998, GoNL)
C=0.025 (18/708, HapMap)
C=0.060 (36/600, NorthernSweden)
C=0.056 (12/216, Qatari)
C=0.12 (5/40, GENOME_DK)
C=0.13 (4/30, Ancient Sardinia)
T=0.45 (10/22, SGDP_PRJ)

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	208320	T=0.931725	C=0.068275
European	Sub	181008	T=0.926213	C=0.073787
African	Sub	6912	T=0.9844	C=0.0156
African Others	Sub	264	T=0.996	C=0.004
African American	Sub	6648	T=0.9839	C=0.0161
Asian	Sub	704	T=0.999	C=0.001
East Asian	Sub	558	T=1.000	C=0.000
Other Asian	Sub	146	T=0.993	C=0.007
Latin American 1	Sub	842	T=0.964	C=0.036
Latin American 2	Sub	6848	T=0.9663	C=0.0337
South Asian	Sub	5042	T=0.9802	C=0.0198
Other	Sub	6964	T=0.9430	C=0.0570

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=0.953844	C=0.046156
Allele Frequency Aggregator	Total	Global	208228	T=0.931729	C=0.068271
Allele Frequency Aggregator	European	Sub	180934	T=0.926222	C=0.073778
Allele Frequency Aggregator	Other	Sub	6946	T=0.9428	C=0.0572
Allele Frequency Aggregator	African	Sub	6912	T=0.9844	C=0.0156
Allele Frequency Aggregator	Latin American 2	Sub	6848	T=0.9663	C=0.0337
Allele Frequency Aggregator	South Asian	Sub	5042	T=0.9802	C=0.0198
Allele Frequency Aggregator	Latin American 1	Sub	842	T=0.964	C=0.036
Allele Frequency Aggregator	Asian	Sub	704	T=0.999	C=0.001
gnomAD - Genomes	Global	Study-wide	140226	T=0.949831	C=0.050169
gnomAD - Genomes	European	Sub	75926	T=0.92620	C=0.07380
gnomAD - Genomes	African	Sub	42050	T=0.98552	C=0.01448
gnomAD - Genomes	American	Sub	13650	T=0.96110	C=0.03890
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	T=0.9395	C=0.0605
gnomAD - Genomes	East Asian	Sub	3132	T=0.9997	C=0.0003
gnomAD - Genomes	Other	Sub	2148	T=0.9581	C=0.0419
1000Genomes_30x	Global	Study-wide	6404	T=0.9788	C=0.0212
1000Genomes_30x	African	Sub	1786	T=0.9955	C=0.0045
1000Genomes_30x	Europe	Sub	1266	T=0.9336	C=0.0664
1000Genomes_30x	South Asian	Sub	1202	T=0.9825	C=0.0175
1000Genomes_30x	East Asian	Sub	1170	T=1.0000	C=0.0000
1000Genomes_30x	American	Sub	980	T=0.977	C=0.023
1000Genomes	Global	Study-wide	5008	T=0.9786	C=0.0214
1000Genomes	African	Sub	1322	T=0.9955	C=0.0045
1000Genomes	East Asian	Sub	1008	T=1.0000	C=0.0000
1000Genomes	Europe	Sub	1006	T=0.9334	C=0.0666
1000Genomes	South Asian	Sub	978	T=0.984	C=0.016
1000Genomes	American	Sub	694	T=0.974	C=0.026
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.9201	C=0.0799
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9292	C=0.0708
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9264	C=0.0736
KOREAN population from KRGDB	KOREAN	Study-wide	2922	T=0.9997	C=0.0003
HGDP-CEPH-db Supplement 1	Global	Study-wide	2084	T=0.9741	C=0.0259
HGDP-CEPH-db Supplement 1	Est_Asia	Sub	470	T=1.000	C=0.000
HGDP-CEPH-db Supplement 1	Central_South_Asia	Sub	414	T=0.988	C=0.012
HGDP-CEPH-db Supplement 1	Middle_Est	Sub	350	T=0.911	C=0.089
HGDP-CEPH-db Supplement 1	Europe	Sub	320	T=0.947	C=0.053
HGDP-CEPH-db Supplement 1	Africa	Sub	242	T=0.996	C=0.004
HGDP-CEPH-db Supplement 1	America	Sub	216	T=1.000	C=0.000
HGDP-CEPH-db Supplement 1	Oceania	Sub	72	T=1.00	C=0.00
Genome-wide autozygosity in Daghestan	Global	Study-wide	1136	T=0.9639	C=0.0361
Genome-wide autozygosity in Daghestan	Daghestan	Sub	628	T=0.970	C=0.030
Genome-wide autozygosity in Daghestan	Near_East	Sub	144	T=0.972	C=0.028
Genome-wide autozygosity in Daghestan	Central Asia	Sub	122	T=0.959	C=0.041
Genome-wide autozygosity in Daghestan	Europe	Sub	108	T=0.907	C=0.093
Genome-wide autozygosity in Daghestan	South Asian	Sub	98	T=0.98	C=0.02
Genome-wide autozygosity in Daghestan	Caucasus	Sub	36	T=0.97	C=0.03
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.931	C=0.069
HapMap	Global	Study-wide	708	T=0.975	C=0.025
HapMap	African	Sub	402	T=0.995	C=0.005
HapMap	American	Sub	218	T=0.927	C=0.073
HapMap	Asian	Sub	88	T=1.00	C=0.00
Northern Sweden	ACPOP	Study-wide	600	T=0.940	C=0.060
Qatari	Global	Study-wide	216	T=0.944	C=0.056
The Danish reference pan genome	Danish	Study-wide	40	T=0.88	C=0.12
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	30	T=0.87	C=0.13
SGDP_PRJ	Global	Study-wide	22	T=0.45	C=0.55

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 18	NC_000018.10:g.2461961T>C
GRCh37.p13 chr 18	NC_000018.9:g.2461960T>C

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=	C
GRCh38.p14 chr 18	NC_000018.10:g.2461961=	NC_000018.10:g.2461961T>C
GRCh37.p13 chr 18	NC_000018.9:g.2461960=	NC_000018.9:g.2461960T>C

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#.

85 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WUGSC_SSAHASNP	ss14026690	Dec 05, 2003 (119)
2	ILLUMINA	ss66873589	Nov 29, 2006 (127)
3	ILLUMINA	ss66954323	Nov 29, 2006 (127)
4	ILLUMINA	ss68079943	Dec 12, 2006 (127)
5	ILLUMINA	ss70469114	May 26, 2008 (130)
6	ILLUMINA	ss70990672	May 16, 2007 (127)
7	ILLUMINA	ss75582393	Dec 06, 2007 (129)
8	KRIBB_YJKIM	ss84915407	Dec 15, 2007 (130)
9	1000GENOMES	ss110044473	Jan 24, 2009 (130)
10	ILLUMINA	ss152589792	Dec 01, 2009 (131)
11	ILLUMINA	ss159113149	Dec 01, 2009 (131)
12	ILLUMINA	ss159872285	Dec 01, 2009 (131)
13	ILLUMINA	ss169779754	Jul 04, 2010 (132)
14	1000GENOMES	ss237355773	Jul 15, 2010 (132)
15	ILLUMINA	ss479209464	May 04, 2012 (137)
16	ILLUMINA	ss479211942	May 04, 2012 (137)
17	ILLUMINA	ss479555332	Sep 08, 2015 (146)
18	ILLUMINA	ss484405619	May 04, 2012 (137)
19	ILLUMINA	ss536584237	Sep 08, 2015 (146)
20	ILLUMINA	ss778725248	Sep 08, 2015 (146)
21	ILLUMINA	ss782649234	Sep 08, 2015 (146)
22	ILLUMINA	ss783618490	Sep 08, 2015 (146)
23	ILLUMINA	ss831899547	Sep 08, 2015 (146)
24	ILLUMINA	ss832625896	Jul 13, 2019 (153)
25	ILLUMINA	ss834184683	Sep 08, 2015 (146)
26	EVA-GONL	ss993424734	Aug 21, 2014 (142)
27	1000GENOMES	ss1359883990	Aug 21, 2014 (142)
28	HAMMER_LAB	ss1397736973	Sep 08, 2015 (146)
29	EVA_GENOME_DK	ss1578282125	Apr 01, 2015 (144)
30	EVA_UK10K_ALSPAC	ss1636277583	Apr 01, 2015 (144)
31	EVA_UK10K_TWINSUK	ss1679271616	Apr 01, 2015 (144)
32	EVA_DECODE	ss1697476106	Apr 01, 2015 (144)
33	EVA_SVP	ss1713604288	Apr 01, 2015 (144)
34	ILLUMINA	ss1752250431	Sep 08, 2015 (146)
35	WEILL_CORNELL_DGM	ss1936895121	Feb 12, 2016 (147)
36	JJLAB	ss2029218802	Sep 14, 2016 (149)
37	HUMAN_LONGEVITY	ss2219324651	Dec 20, 2016 (150)
38	ILLUMINA	ss2633437541	Nov 08, 2017 (151)
39	ILLUMINA	ss2635075860	Nov 08, 2017 (151)
40	GNOMAD	ss2953433387	Nov 08, 2017 (151)
41	AFFY	ss2985110043	Nov 08, 2017 (151)
42	AFFY	ss2985744671	Nov 08, 2017 (151)
43	SWEGEN	ss3016055691	Nov 08, 2017 (151)
44	CSHL	ss3351886533	Nov 08, 2017 (151)
45	ILLUMINA	ss3627744939	Oct 12, 2018 (152)
46	ILLUMINA	ss3631415813	Oct 12, 2018 (152)
47	ILLUMINA	ss3633151863	Oct 12, 2018 (152)
48	ILLUMINA	ss3633860245	Oct 12, 2018 (152)
49	ILLUMINA	ss3634692879	Oct 12, 2018 (152)
50	ILLUMINA	ss3635547766	Oct 12, 2018 (152)
51	ILLUMINA	ss3636380984	Oct 12, 2018 (152)
52	ILLUMINA	ss3637299336	Oct 12, 2018 (152)
53	ILLUMINA	ss3638180058	Oct 12, 2018 (152)
54	ILLUMINA	ss3639097915	Oct 12, 2018 (152)
55	ILLUMINA	ss3639856970	Oct 12, 2018 (152)
56	ILLUMINA	ss3640400189	Oct 12, 2018 (152)
57	ILLUMINA	ss3643156976	Oct 12, 2018 (152)
58	ILLUMINA	ss3643906249	Oct 12, 2018 (152)
59	BIOINF_KMB_FNS_UNIBA	ss3645471177	Oct 12, 2018 (152)
60	ILLUMINA	ss3653882253	Oct 12, 2018 (152)
61	EGCUT_WGS	ss3682909982	Jul 13, 2019 (153)
62	EVA_DECODE	ss3701095546	Jul 13, 2019 (153)
63	ACPOP	ss3742296180	Jul 13, 2019 (153)
64	ILLUMINA	ss3744993076	Jul 13, 2019 (153)
65	EVA	ss3755042186	Jul 13, 2019 (153)
66	ILLUMINA	ss3772490664	Jul 13, 2019 (153)
67	KHV_HUMAN_GENOMES	ss3820305712	Jul 13, 2019 (153)
68	EVA	ss3835025390	Apr 27, 2020 (154)
69	EVA	ss3841126442	Apr 27, 2020 (154)
70	EVA	ss3846625756	Apr 27, 2020 (154)
71	HGDP	ss3847573399	Apr 27, 2020 (154)
72	SGDP_PRJ	ss3886415045	Apr 27, 2020 (154)
73	KRGDB	ss3936218105	Apr 27, 2020 (154)
74	EVA	ss3985808323	Apr 27, 2021 (155)
75	EVA	ss4017782973	Apr 27, 2021 (155)
76	TOPMED	ss5046646331	Apr 27, 2021 (155)
77	1000G_HIGH_COVERAGE	ss5304252045	Oct 16, 2022 (156)
78	EVA	ss5429590406	Oct 16, 2022 (156)
79	HUGCELL_USP	ss5497178689	Oct 16, 2022 (156)
80	1000G_HIGH_COVERAGE	ss5608484939	Oct 16, 2022 (156)
81	SANFORD_IMAGENETICS	ss5660719843	Oct 16, 2022 (156)
82	EVA	ss5799984519	Oct 16, 2022 (156)
83	EVA	ss5827153083	Oct 16, 2022 (156)
84	EVA	ss5872950106	Oct 16, 2022 (156)
85	EVA	ss5952118185	Oct 16, 2022 (156)
86	1000Genomes	NC_000018.9 - 2461960	Oct 12, 2018 (152)
87	1000Genomes_30x	NC_000018.10 - 2461961	Oct 16, 2022 (156)
88	The Avon Longitudinal Study of Parents and Children	NC_000018.9 - 2461960	Oct 12, 2018 (152)
89	Genome-wide autozygosity in Daghestan	NC_000018.8 - 2451960	Apr 27, 2020 (154)
90	Genetic variation in the Estonian population	NC_000018.9 - 2461960	Oct 12, 2018 (152)
91	The Danish reference pan genome	NC_000018.9 - 2461960	Apr 27, 2020 (154)
92	gnomAD - Genomes	NC_000018.10 - 2461961	Apr 27, 2021 (155)
93	Genome of the Netherlands Release 5	NC_000018.9 - 2461960	Apr 27, 2020 (154)
94	HGDP-CEPH-db Supplement 1	NC_000018.8 - 2451960	Apr 27, 2020 (154)
95	HapMap	NC_000018.10 - 2461961	Apr 27, 2020 (154)
96	KOREAN population from KRGDB	NC_000018.9 - 2461960	Apr 27, 2020 (154)
97	Northern Sweden	NC_000018.9 - 2461960	Jul 13, 2019 (153)
98	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000018.9 - 2461960	Apr 27, 2021 (155)
99	Qatari	NC_000018.9 - 2461960	Apr 27, 2020 (154)
100	SGDP_PRJ	NC_000018.9 - 2461960	Apr 27, 2020 (154)
101	TopMed	NC_000018.10 - 2461961	Apr 27, 2021 (155)
102	UK 10K study - Twins	NC_000018.9 - 2461960	Oct 12, 2018 (152)
103	ALFA	NC_000018.10 - 2461961	Apr 27, 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)
rs60701282	May 26, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
206780, 251291, ss110044473, ss479209464, ss1397736973, ss1697476106, ss1713604288, ss2635075860, ss3639097915, ss3639856970, ss3643156976, ss3643906249, ss3847573399	NC_000018.8:2451959:T:C	NC_000018.10:2461960:T:C	(self)
73172612, 40541923, 28648230, 4479205, 18060526, 43395499, 15581045, 1034250, 18937043, 38432025, 40541923, ss237355773, ss479211942, ss479555332, ss484405619, ss536584237, ss778725248, ss782649234, ss783618490, ss831899547, ss832625896, ss834184683, ss993424734, ss1359883990, ss1578282125, ss1636277583, ss1679271616, ss1752250431, ss1936895121, ss2029218802, ss2633437541, ss2953433387, ss2985110043, ss2985744671, ss3016055691, ss3351886533, ss3627744939, ss3631415813, ss3633151863, ss3633860245, ss3634692879, ss3635547766, ss3636380984, ss3637299336, ss3638180058, ss3640400189, ss3653882253, ss3682909982, ss3742296180, ss3744993076, ss3755042186, ss3772490664, ss3835025390, ss3841126442, ss3886415045, ss3936218105, ss3985808323, ss4017782973, ss5429590406, ss5660719843, ss5799984519, ss5827153083, ss5952118185	NC_000018.9:2461959:T:C	NC_000018.10:2461960:T:C	(self)
96010874, 516301625, 1540841, 262191994, 15818558824, ss2219324651, ss3645471177, ss3701095546, ss3820305712, ss3846625756, ss5046646331, ss5304252045, ss5497178689, ss5608484939, ss5872950106	NC_000018.10:2461960:T:C	NC_000018.10:2461960:T:C	(self)
ss14026690	NT_010859.13:2451959:T:C	NC_000018.10:2461960:T:C	(self)
ss66873589, ss66954323, ss68079943, ss70469114, ss70990672, ss75582393, ss84915407, ss152589792, ss159113149, ss159872285, ss169779754	NT_010859.14:2451959:T:C	NC_000018.10:2461960:T:C	(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 rs10164009

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

rs10164009