Name: rs7099702
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.

rs7099702

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr10:95292537 (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
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.185931 (49214/264690, TOPMED)
T=0.187933 (26329/140098, GnomAD)
T=0.15791 (12422/78664, PAGE_STUDY) (+ 17 more)
T=0.18962 (5995/31616, ALFA)
T=0.00000 (0/28258, 14KJPN)
T=0.00000 (0/16760, 8.3KJPN)
T=0.1362 (872/6404, 1000G_30x)
T=0.1312 (657/5008, 1000G)
T=0.1556 (697/4480, Estonian)
T=0.1959 (755/3854, ALSPAC)
T=0.2047 (759/3708, TWINSUK)
T=0.0007 (2/2930, KOREAN)
T=0.0000 (0/1832, Korea1K)
T=0.213 (213/998, GoNL)
T=0.165 (99/600, NorthernSweden)
T=0.086 (46/538, SGDP_PRJ)
T=0.259 (56/216, Qatari)
T=0.014 (3/212, Vietnamese)
T=0.06 (3/54, Siberian)
T=0.07 (3/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: PDLIM1 : 2KB Upstream Variant
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	31616	T=0.18962	C=0.81038
European	Sub	24810	T=0.19017	C=0.80983
African	Sub	3600	T=0.2053	C=0.7947
African Others	Sub	124	T=0.202	C=0.798
African American	Sub	3476	T=0.2054	C=0.7946
Asian	Sub	162	T=0.006	C=0.994
East Asian	Sub	134	T=0.000	C=1.000
Other Asian	Sub	28	T=0.04	C=0.96
Latin American 1	Sub	168	T=0.202	C=0.798
Latin American 2	Sub	700	T=0.126	C=0.874
South Asian	Sub	120	T=0.100	C=0.900
Other	Sub	2056	T=0.1960	C=0.8040

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=0.185931	C=0.814069
gnomAD - Genomes	Global	Study-wide	140098	T=0.187933	C=0.812067
gnomAD - Genomes	European	Sub	75860	T=0.18857	C=0.81143
gnomAD - Genomes	African	Sub	41982	T=0.21242	C=0.78758
gnomAD - Genomes	American	Sub	13656	T=0.14748	C=0.85252
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	T=0.2185	C=0.7815
gnomAD - Genomes	East Asian	Sub	3132	T=0.0003	C=0.9997
gnomAD - Genomes	Other	Sub	2146	T=0.1701	C=0.8299
The PAGE Study	Global	Study-wide	78664	T=0.15791	C=0.84209
The PAGE Study	AfricanAmerican	Sub	32498	T=0.20980	C=0.79020
The PAGE Study	Mexican	Sub	10810	T=0.12377	C=0.87623
The PAGE Study	Asian	Sub	8316	T=0.0022	C=0.9978
The PAGE Study	PuertoRican	Sub	7914	T=0.1813	C=0.8187
The PAGE Study	NativeHawaiian	Sub	4532	T=0.0596	C=0.9404
The PAGE Study	Cuban	Sub	4222	T=0.2158	C=0.7842
The PAGE Study	Dominican	Sub	3828	T=0.2181	C=0.7819
The PAGE Study	CentralAmerican	Sub	2448	T=0.1066	C=0.8934
The PAGE Study	SouthAmerican	Sub	1980	T=0.1146	C=0.8854
The PAGE Study	NativeAmerican	Sub	1260	T=0.1667	C=0.8333
The PAGE Study	SouthAsian	Sub	856	T=0.116	C=0.884
Allele Frequency Aggregator	Total	Global	31616	T=0.18962	C=0.81038
Allele Frequency Aggregator	European	Sub	24810	T=0.19017	C=0.80983
Allele Frequency Aggregator	African	Sub	3600	T=0.2053	C=0.7947
Allele Frequency Aggregator	Other	Sub	2056	T=0.1960	C=0.8040
Allele Frequency Aggregator	Latin American 2	Sub	700	T=0.126	C=0.874
Allele Frequency Aggregator	Latin American 1	Sub	168	T=0.202	C=0.798
Allele Frequency Aggregator	Asian	Sub	162	T=0.006	C=0.994
Allele Frequency Aggregator	South Asian	Sub	120	T=0.100	C=0.900
14KJPN	JAPANESE	Study-wide	28258	T=0.00000	C=1.00000
8.3KJPN	JAPANESE	Study-wide	16760	T=0.00000	C=1.00000
1000Genomes_30x	Global	Study-wide	6404	T=0.1362	C=0.8638
1000Genomes_30x	African	Sub	1786	T=0.2088	C=0.7912
1000Genomes_30x	Europe	Sub	1266	T=0.1904	C=0.8096
1000Genomes_30x	South Asian	Sub	1202	T=0.1048	C=0.8952
1000Genomes_30x	East Asian	Sub	1170	T=0.0017	C=0.9983
1000Genomes_30x	American	Sub	980	T=0.133	C=0.867
1000Genomes	Global	Study-wide	5008	T=0.1312	C=0.8688
1000Genomes	African	Sub	1322	T=0.2065	C=0.7935
1000Genomes	East Asian	Sub	1008	T=0.0010	C=0.9990
1000Genomes	Europe	Sub	1006	T=0.1889	C=0.8111
1000Genomes	South Asian	Sub	978	T=0.105	C=0.895
1000Genomes	American	Sub	694	T=0.130	C=0.870
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.1556	C=0.8444
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.1959	C=0.8041
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.2047	C=0.7953
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.0007	A=0.0000, C=0.9993
Korean Genome Project	KOREAN	Study-wide	1832	T=0.0000	C=1.0000
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.213	C=0.787
Northern Sweden	ACPOP	Study-wide	600	T=0.165	C=0.835
SGDP_PRJ	Global	Study-wide	538	T=0.086	C=0.914
Qatari	Global	Study-wide	216	T=0.259	C=0.741
A Vietnamese Genetic Variation Database	Global	Study-wide	212	T=0.014	C=0.986
Siberian	Global	Study-wide	54	T=0.06	C=0.94
The Danish reference pan genome	Danish	Study-wide	40	T=0.07	C=0.93

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 10	NC_000010.11:g.95292537T>A
GRCh38.p14 chr 10	NC_000010.11:g.95292537T>C
GRCh37.p13 chr 10	NC_000010.10:g.97052294T>A
GRCh37.p13 chr 10	NC_000010.10:g.97052294T>C

Gene: PDLIM1, PDZ and LIM domain 1 (minus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
PDLIM1 transcript	NM_020992.4:c.	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	T=	A	C
GRCh38.p14 chr 10	NC_000010.11:g.95292537=	NC_000010.11:g.95292537T>A	NC_000010.11:g.95292537T>C
GRCh37.p13 chr 10	NC_000010.10:g.97052294=	NC_000010.10:g.97052294T>A	NC_000010.10:g.97052294T>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#.

92 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCM_SSAHASNP	ss10642187	Jul 11, 2003 (116)
2	SC_SNP	ss15882104	Feb 27, 2004 (120)
3	CSHL-HAPMAP	ss16467218	Feb 27, 2004 (120)
4	CSHL-HAPMAP	ss19158337	Feb 27, 2004 (120)
5	CSHL-HAPMAP	ss19876517	Feb 27, 2004 (120)
6	ABI	ss39730805	Mar 15, 2006 (126)
7	EGP_SNPS	ss70437746	May 17, 2007 (127)
8	HGSV	ss83145839	Dec 14, 2007 (130)
9	BCMHGSC_JDW	ss88318500	Mar 23, 2008 (129)
10	BGI	ss106695997	Feb 03, 2009 (130)
11	1000GENOMES	ss109670820	Jan 24, 2009 (130)
12	1000GENOMES	ss113676972	Jan 25, 2009 (130)
13	ILLUMINA-UK	ss119276783	Feb 15, 2009 (130)
14	ENSEMBL	ss132021620	Dec 01, 2009 (131)
15	GMI	ss155408647	Dec 01, 2009 (131)
16	ENSEMBL	ss161373779	Dec 01, 2009 (131)
17	COMPLETE_GENOMICS	ss168690402	Jul 04, 2010 (132)
18	COMPLETE_GENOMICS	ss170782566	Jul 04, 2010 (132)
19	COMPLETE_GENOMICS	ss174705125	Jul 04, 2010 (132)
20	BUSHMAN	ss201891033	Jul 04, 2010 (132)
21	BCM-HGSC-SUB	ss207145214	Jul 04, 2010 (132)
22	1000GENOMES	ss224885843	Jul 14, 2010 (132)
23	1000GENOMES	ss235294094	Jul 15, 2010 (132)
24	1000GENOMES	ss241976850	Jul 15, 2010 (132)
25	GMI	ss280733617	May 04, 2012 (137)
26	GMI	ss286244544	Apr 25, 2013 (138)
27	PJP	ss290910095	May 09, 2011 (134)
28	ILLUMINA	ss482694299	May 04, 2012 (137)
29	ILLUMINA	ss483941744	May 04, 2012 (137)
30	ILLUMINA	ss536135844	Sep 08, 2015 (146)
31	TISHKOFF	ss562144897	Apr 25, 2013 (138)
32	SSMP	ss657188860	Apr 25, 2013 (138)
33	ILLUMINA	ss780466239	Sep 08, 2015 (146)
34	ILLUMINA	ss782414723	Sep 08, 2015 (146)
35	ILLUMINA	ss835956462	Sep 08, 2015 (146)
36	EVA-GONL	ss987808959	Aug 21, 2014 (142)
37	JMKIDD_LAB	ss1077218481	Aug 21, 2014 (142)
38	1000GENOMES	ss1338640324	Aug 21, 2014 (142)
39	DDI	ss1426412439	Apr 01, 2015 (144)
40	EVA_GENOME_DK	ss1575298719	Apr 01, 2015 (144)
41	EVA_DECODE	ss1597482110	Apr 01, 2015 (144)
42	EVA_UK10K_ALSPAC	ss1625204145	Apr 01, 2015 (144)
43	EVA_UK10K_TWINSUK	ss1668198178	Apr 01, 2015 (144)
44	HAMMER_LAB	ss1806521877	Sep 08, 2015 (146)
45	WEILL_CORNELL_DGM	ss1931175043	Feb 12, 2016 (147)
46	ILLUMINA	ss1959285271	Feb 12, 2016 (147)
47	GENOMED	ss1967200421	Jul 19, 2016 (147)
48	JJLAB	ss2026315832	Sep 14, 2016 (149)
49	USC_VALOUEV	ss2154592597	Nov 08, 2017 (151)
50	HUMAN_LONGEVITY	ss2177178764	Dec 20, 2016 (150)
51	SYSTEMSBIOZJU	ss2627626498	Nov 08, 2017 (151)
52	ILLUMINA	ss2632748919	Nov 08, 2017 (151)
53	GRF	ss2698845462	Nov 08, 2017 (151)
54	GNOMAD	ss2892174983	Nov 08, 2017 (151)
55	SWEGEN	ss3006973151	Nov 08, 2017 (151)
56	ILLUMINA	ss3021265169	Nov 08, 2017 (151)
57	BIOINF_KMB_FNS_UNIBA	ss3026948083	Nov 08, 2017 (151)
58	CSHL	ss3349263178	Nov 08, 2017 (151)
59	ILLUMINA	ss3626510645	Oct 12, 2018 (152)
60	ILLUMINA	ss3630772085	Oct 12, 2018 (152)
61	ILLUMINA	ss3641694342	Oct 12, 2018 (152)
62	ILLUMINA	ss3651623604	Oct 12, 2018 (152)
63	EGCUT_WGS	ss3674384787	Jul 13, 2019 (153)
64	EVA_DECODE	ss3690469444	Jul 13, 2019 (153)
65	ILLUMINA	ss3725179735	Jul 13, 2019 (153)
66	ACPOP	ss3737589119	Jul 13, 2019 (153)
67	EVA	ss3748473286	Jul 13, 2019 (153)
68	PAGE_CC	ss3771575897	Jul 13, 2019 (153)
69	PACBIO	ss3786757908	Jul 13, 2019 (153)
70	PACBIO	ss3791925165	Jul 13, 2019 (153)
71	PACBIO	ss3796807284	Jul 13, 2019 (153)
72	KHV_HUMAN_GENOMES	ss3813840120	Jul 13, 2019 (153)
73	EVA	ss3832278680	Apr 26, 2020 (154)
74	EVA	ss3839680742	Apr 26, 2020 (154)
75	EVA	ss3845154443	Apr 26, 2020 (154)
76	SGDP_PRJ	ss3874836053	Apr 26, 2020 (154)
77	KRGDB	ss3922965576	Apr 26, 2020 (154)
78	KOGIC	ss3968466037	Apr 26, 2020 (154)
79	TOPMED	ss4862772845	Apr 26, 2021 (155)
80	TOMMO_GENOMICS	ss5198987088	Apr 26, 2021 (155)
81	1000G_HIGH_COVERAGE	ss5285102327	Oct 16, 2022 (156)
82	EVA	ss5315494764	Oct 16, 2022 (156)
83	EVA	ss5395347090	Oct 16, 2022 (156)
84	HUGCELL_USP	ss5480559005	Oct 16, 2022 (156)
85	1000G_HIGH_COVERAGE	ss5579586983	Oct 16, 2022 (156)
86	SANFORD_IMAGENETICS	ss5649894266	Oct 16, 2022 (156)
87	TOMMO_GENOMICS	ss5745210540	Oct 16, 2022 (156)
88	YY_MCH	ss5811796005	Oct 16, 2022 (156)
89	EVA	ss5824812622	Oct 16, 2022 (156)
90	EVA	ss5849698578	Oct 16, 2022 (156)
91	EVA	ss5880101458	Oct 16, 2022 (156)
92	EVA	ss5941180599	Oct 16, 2022 (156)
93	1000Genomes	NC_000010.10 - 97052294	Oct 12, 2018 (152)
94	1000Genomes_30x	NC_000010.11 - 95292537	Oct 16, 2022 (156)
95	The Avon Longitudinal Study of Parents and Children	NC_000010.10 - 97052294	Oct 12, 2018 (152)
96	Genetic variation in the Estonian population	NC_000010.10 - 97052294	Oct 12, 2018 (152)
97	The Danish reference pan genome	NC_000010.10 - 97052294	Apr 26, 2020 (154)
98	gnomAD - Genomes	NC_000010.11 - 95292537	Apr 26, 2021 (155)
99	Genome of the Netherlands Release 5	NC_000010.10 - 97052294	Apr 26, 2020 (154)
100	KOREAN population from KRGDB	NC_000010.10 - 97052294	Apr 26, 2020 (154)
101	Korean Genome Project	NC_000010.11 - 95292537	Apr 26, 2020 (154)
102	Northern Sweden	NC_000010.10 - 97052294	Jul 13, 2019 (153)
103	The PAGE Study	NC_000010.11 - 95292537	Jul 13, 2019 (153)
104	Qatari	NC_000010.10 - 97052294	Apr 26, 2020 (154)
105	SGDP_PRJ	NC_000010.10 - 97052294	Apr 26, 2020 (154)
106	Siberian	NC_000010.10 - 97052294	Apr 26, 2020 (154)
107	8.3KJPN	NC_000010.10 - 97052294	Apr 26, 2021 (155)
108	14KJPN	NC_000010.11 - 95292537	Oct 16, 2022 (156)
109	TopMed	NC_000010.11 - 95292537	Apr 26, 2021 (155)
110	UK 10K study - Twins	NC_000010.10 - 97052294	Oct 12, 2018 (152)
111	A Vietnamese Genetic Variation Database	NC_000010.10 - 97052294	Jul 13, 2019 (153)
112	ALFA	NC_000010.11 - 95292537	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).

Associated ID	History Updated (Build)
rs57027427	May 23, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
30142970, ss3922965576	NC_000010.10:97052293:T:A	NC_000010.11:95292536:T:A	(self)
ss83145839	NC_000010.8:97042283:T:C	NC_000010.11:95292536:T:C	(self)
ss88318500, ss109670820, ss113676972, ss119276783, ss168690402, ss170782566, ss174705125, ss201891033, ss207145214, ss280733617, ss286244544, ss290910095, ss482694299, ss1597482110	NC_000010.9:97042283:T:C	NC_000010.11:95292536:T:C	(self)
51072325, 28354429, 20123035, 2284293, 12643695, 30142970, 10873984, 13216973, 26853033, 7108951, 56956395, 28354429, 6296417, ss224885843, ss235294094, ss241976850, ss483941744, ss536135844, ss562144897, ss657188860, ss780466239, ss782414723, ss835956462, ss987808959, ss1077218481, ss1338640324, ss1426412439, ss1575298719, ss1625204145, ss1668198178, ss1806521877, ss1931175043, ss1959285271, ss1967200421, ss2026315832, ss2154592597, ss2627626498, ss2632748919, ss2698845462, ss2892174983, ss3006973151, ss3021265169, ss3349263178, ss3626510645, ss3630772085, ss3641694342, ss3651623604, ss3674384787, ss3737589119, ss3748473286, ss3786757908, ss3791925165, ss3796807284, ss3832278680, ss3839680742, ss3874836053, ss3922965576, ss5198987088, ss5315494764, ss5395347090, ss5649894266, ss5824812622, ss5941180599	NC_000010.10:97052293:T:C	NC_000010.11:95292536:T:C	(self)
67112918, 360855952, 24844038, 797366, 79047644, 78318500, 6131860701, ss2177178764, ss3026948083, ss3690469444, ss3725179735, ss3771575897, ss3813840120, ss3845154443, ss3968466037, ss4862772845, ss5285102327, ss5480559005, ss5579586983, ss5745210540, ss5811796005, ss5849698578, ss5880101458	NC_000010.11:95292536:T:C	NC_000010.11:95292536:T:C	(self)
ss10642187	NT_030059.10:15490851:T:C	NC_000010.11:95292536:T:C	(self)
ss15882104, ss16467218, ss19158337, ss19876517	NT_030059.11:15800819:T:C	NC_000010.11:95292536:T:C	(self)
ss39730805, ss70437746, ss106695997, ss132021620, ss155408647, ss161373779	NT_030059.13:47856757:T:C	NC_000010.11:95292536: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 rs7099702

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

rs7099702