Name: rs15
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.

rs15

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr7:11563305 (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>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.150168 (39748/264690, TOPMED)
C=0.18094 (5113/28258, 14KJPN)
C=0.17902 (3000/16758, 8.3KJPN) (+ 16 more)
C=0.2701 (2328/8620, ALFA)
C=0.1529 (979/6404, 1000G_30x)
C=0.1591 (797/5008, 1000G)
C=0.2667 (1195/4480, Estonian)
C=0.2270 (875/3854, ALSPAC)
C=0.2257 (837/3708, TWINSUK)
C=0.2143 (628/2930, KOREAN)
C=0.2172 (398/1832, Korea1K)
C=0.288 (287/998, GoNL)
C=0.263 (158/600, NorthernSweden)
C=0.149 (79/530, SGDP_PRJ)
C=0.109 (36/330, HapMap)
C=0.139 (30/216, Qatari)
C=0.231 (49/212, Vietnamese)
C=0.26 (14/54, Siberian)
C=0.20 (8/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: THSD7A : Intron Variant
Publications: 1 citation
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	8620	C=0.2701	G=0.0000, T=0.7299
European	Sub	7686	C=0.2870	G=0.0000, T=0.7130
African	Sub	654	C=0.038	G=0.000, T=0.962
African Others	Sub	30	C=0.00	G=0.00, T=1.00
African American	Sub	624	C=0.040	G=0.000, T=0.960
Asian	Sub	12	C=0.75	G=0.00, T=0.25
East Asian	Sub	10	C=0.9	G=0.0, T=0.1
Other Asian	Sub	2	C=0.0	G=0.0, T=1.0
Latin American 1	Sub	4	C=1.0	G=0.0, T=0.0
Latin American 2	Sub	8	C=1.0	G=0.0, T=0.0
South Asian	Sub	10	C=0.9	G=0.0, T=0.1
Other	Sub	246	C=0.272	G=0.000, T=0.728

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=0.150168	T=0.849832
14KJPN	JAPANESE	Study-wide	28258	C=0.18094	T=0.81906
8.3KJPN	JAPANESE	Study-wide	16758	C=0.17902	T=0.82098
Allele Frequency Aggregator	Total	Global	8620	C=0.2701	G=0.0000, T=0.7299
Allele Frequency Aggregator	European	Sub	7686	C=0.2870	G=0.0000, T=0.7130
Allele Frequency Aggregator	African	Sub	654	C=0.038	G=0.000, T=0.962
Allele Frequency Aggregator	Other	Sub	246	C=0.272	G=0.000, T=0.728
Allele Frequency Aggregator	Asian	Sub	12	C=0.75	G=0.00, T=0.25
Allele Frequency Aggregator	South Asian	Sub	10	C=0.9	G=0.0, T=0.1
Allele Frequency Aggregator	Latin American 2	Sub	8	C=1.0	G=0.0, T=0.0
Allele Frequency Aggregator	Latin American 1	Sub	4	C=1.0	G=0.0, T=0.0
1000Genomes_30x	Global	Study-wide	6404	C=0.1529	T=0.8471
1000Genomes_30x	African	Sub	1786	C=0.0112	T=0.9888
1000Genomes_30x	Europe	Sub	1266	C=0.2180	T=0.7820
1000Genomes_30x	South Asian	Sub	1202	C=0.2662	T=0.7338
1000Genomes_30x	East Asian	Sub	1170	C=0.2282	T=0.7718
1000Genomes_30x	American	Sub	980	C=0.098	T=0.902
1000Genomes	Global	Study-wide	5008	C=0.1591	T=0.8409
1000Genomes	African	Sub	1322	C=0.0121	T=0.9879
1000Genomes	East Asian	Sub	1008	C=0.2302	T=0.7698
1000Genomes	Europe	Sub	1006	C=0.2127	T=0.7873
1000Genomes	South Asian	Sub	978	C=0.267	T=0.733
1000Genomes	American	Sub	694	C=0.107	T=0.893
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.2667	T=0.7333
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.2270	T=0.7730
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.2257	T=0.7743
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.2143	T=0.7857
Korean Genome Project	KOREAN	Study-wide	1832	C=0.2172	T=0.7828
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.288	T=0.712
Northern Sweden	ACPOP	Study-wide	600	C=0.263	T=0.737
SGDP_PRJ	Global	Study-wide	530	C=0.149	T=0.851
HapMap	Global	Study-wide	330	C=0.109	T=0.891
HapMap	African	Sub	120	C=0.000	T=1.000
HapMap	American	Sub	120	C=0.225	T=0.775
HapMap	Asian	Sub	90	C=0.10	T=0.90
Qatari	Global	Study-wide	216	C=0.139	T=0.861
A Vietnamese Genetic Variation Database	Global	Study-wide	212	C=0.231	T=0.769
Siberian	Global	Study-wide	54	C=0.26	T=0.74
The Danish reference pan genome	Danish	Study-wide	40	C=0.20	T=0.80

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 7	NC_000007.14:g.11563305C>G
GRCh38.p14 chr 7	NC_000007.14:g.11563305C>T
GRCh37.p13 chr 7	NC_000007.13:g.11602932C>G
GRCh37.p13 chr 7	NC_000007.13:g.11602932C>T
THSD7A RefSeqGene	NG_027670.2:g.273893G>C
THSD7A RefSeqGene	NG_027670.2:g.273893G>A
THSD7A RefSeqGene	NG_027670.1:g.273893G>C
THSD7A RefSeqGene	NG_027670.1:g.273893G>A

Gene: THSD7A, thrombospondin type 1 domain containing 7A (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
THSD7A transcript	NM_015204.3:c.1454-20188G… NM_015204.3:c.1454-20188G>C	N/A	Intron Variant
THSD7A transcript variant X1	XM_006715659.2:c.1454-201… XM_006715659.2:c.1454-20188G>C	N/A	Intron Variant
THSD7A transcript variant X4	XM_006715660.2:c.1454-201… XM_006715660.2:c.1454-20188G>C	N/A	Intron Variant
THSD7A transcript variant X5	XM_006715662.2:c.1454-201… XM_006715662.2:c.1454-20188G>C	N/A	Intron Variant
THSD7A transcript variant X2	XM_047420039.1:c.1247-201… XM_047420039.1:c.1247-20188G>C	N/A	Intron Variant
THSD7A transcript variant X3	XM_047420040.1:c.1247-201… XM_047420040.1:c.1247-20188G>C	N/A	Intron 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	C=	G	T
GRCh38.p14 chr 7	NC_000007.14:g.11563305=	NC_000007.14:g.11563305C>G	NC_000007.14:g.11563305C>T
GRCh37.p13 chr 7	NC_000007.13:g.11602932=	NC_000007.13:g.11602932C>G	NC_000007.13:g.11602932C>T
THSD7A RefSeqGene	NG_027670.2:g.273893=	NG_027670.2:g.273893G>C	NG_027670.2:g.273893G>A
THSD7A RefSeqGene	NG_027670.1:g.273893=	NG_027670.1:g.273893G>C	NG_027670.1:g.273893G>A
THSD7A transcript	NM_015204.2:c.1454-20188=	NM_015204.2:c.1454-20188G>C	NM_015204.2:c.1454-20188G>A
THSD7A transcript	NM_015204.3:c.1454-20188=	NM_015204.3:c.1454-20188G>C	NM_015204.3:c.1454-20188G>A
THSD7A transcript variant X1	XM_006715659.2:c.1454-20188=	XM_006715659.2:c.1454-20188G>C	XM_006715659.2:c.1454-20188G>A
THSD7A transcript variant X4	XM_006715660.2:c.1454-20188=	XM_006715660.2:c.1454-20188G>C	XM_006715660.2:c.1454-20188G>A
THSD7A transcript variant X5	XM_006715662.2:c.1454-20188=	XM_006715662.2:c.1454-20188G>C	XM_006715662.2:c.1454-20188G>A
THSD7A transcript variant X2	XM_047420039.1:c.1247-20188=	XM_047420039.1:c.1247-20188G>C	XM_047420039.1:c.1247-20188G>A
THSD7A transcript variant X3	XM_047420040.1:c.1247-20188=	XM_047420040.1:c.1247-20188G>C	XM_047420040.1:c.1247-20188G>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#.

81 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	KWOK	ss14	Sep 19, 2000 (36)
2	BCM_SSAHASNP	ss10419258	Jul 11, 2003 (116)
3	WI_SSAHASNP	ss11907538	Jul 11, 2003 (116)
4	CSHL-HAPMAP	ss17922011	Feb 27, 2004 (120)
5	SSAHASNP	ss22571149	Apr 05, 2004 (121)
6	SSAHASNP	ss22953051	Apr 05, 2004 (121)
7	PERLEGEN	ss24371965	Sep 20, 2004 (126)
8	HGSV	ss77710812	Dec 06, 2007 (129)
9	HGSV	ss85971399	Dec 14, 2007 (130)
10	BCMHGSC_JDW	ss93628225	Mar 24, 2008 (129)
11	HUMANGENOME_JCVI	ss98132681	Feb 04, 2009 (130)
12	BGI	ss105492517	Feb 04, 2009 (130)
13	1000GENOMES	ss111512494	Jan 25, 2009 (130)
14	1000GENOMES	ss113308224	Jan 25, 2009 (130)
15	ILLUMINA-UK	ss115929889	Dec 01, 2009 (131)
16	ENSEMBL	ss139562268	Dec 01, 2009 (131)
17	ENSEMBL	ss142655515	Dec 01, 2009 (131)
18	GMI	ss158041781	Dec 01, 2009 (131)
19	COMPLETE_GENOMICS	ss162049890	Jul 04, 2010 (132)
20	COMPLETE_GENOMICS	ss163638259	Jul 04, 2010 (132)
21	COMPLETE_GENOMICS	ss166139891	Jul 04, 2010 (132)
22	BUSHMAN	ss202942977	Jul 04, 2010 (132)
23	BCM-HGSC-SUB	ss208311583	Jul 04, 2010 (132)
24	1000GENOMES	ss222903810	Jul 14, 2010 (132)
25	1000GENOMES	ss233847427	Jul 15, 2010 (132)
26	1000GENOMES	ss240827740	Jul 15, 2010 (132)
27	BL	ss254050076	May 09, 2011 (134)
28	GMI	ss279184054	May 04, 2012 (137)
29	GMI	ss285573985	Apr 25, 2013 (138)
30	PJP	ss293988670	May 09, 2011 (134)
31	TISHKOFF	ss559802778	Apr 25, 2013 (138)
32	SSMP	ss654151257	Apr 25, 2013 (138)
33	EVA-GONL	ss983943188	Aug 21, 2014 (142)
34	JMKIDD_LAB	ss1074355641	Aug 21, 2014 (142)
35	1000GENOMES	ss1323908031	Aug 21, 2014 (142)
36	DDI	ss1431026827	Apr 01, 2015 (144)
37	EVA_GENOME_DK	ss1582068370	Apr 01, 2015 (144)
38	EVA_DECODE	ss1593507473	Apr 01, 2015 (144)
39	EVA_UK10K_ALSPAC	ss1617560461	Apr 01, 2015 (144)
40	EVA_UK10K_TWINSUK	ss1660554494	Apr 01, 2015 (144)
41	HAMMER_LAB	ss1804864987	Sep 08, 2015 (146)
42	WEILL_CORNELL_DGM	ss1927188614	Feb 12, 2016 (147)
43	GENOMED	ss1970622824	Jul 19, 2016 (147)
44	JJLAB	ss2024265804	Sep 14, 2016 (149)
45	USC_VALOUEV	ss2152464731	Dec 20, 2016 (150)
46	HUMAN_LONGEVITY	ss2291619741	Dec 20, 2016 (150)
47	SYSTEMSBIOZJU	ss2626622626	Nov 08, 2017 (151)
48	GRF	ss2708114976	Nov 08, 2017 (151)
49	GNOMAD	ss2849707227	Nov 08, 2017 (151)
50	SWEGEN	ss3000619748	Nov 08, 2017 (151)
51	BIOINF_KMB_FNS_UNIBA	ss3025926830	Nov 08, 2017 (151)
52	CSHL	ss3347434244	Nov 08, 2017 (151)
53	URBANLAB	ss3648561387	Oct 12, 2018 (152)
54	EGCUT_WGS	ss3668538463	Jul 13, 2019 (153)
55	EVA_DECODE	ss3719091451	Jul 13, 2019 (153)
56	ACPOP	ss3734353203	Jul 13, 2019 (153)
57	EVA	ss3766181574	Jul 13, 2019 (153)
58	PACBIO	ss3785732965	Jul 13, 2019 (153)
59	PACBIO	ss3791047224	Jul 13, 2019 (153)
60	PACBIO	ss3795926921	Jul 13, 2019 (153)
61	KHV_HUMAN_GENOMES	ss3809346912	Jul 13, 2019 (153)
62	EVA	ss3830411382	Apr 26, 2020 (154)
63	EVA	ss3838691771	Apr 26, 2020 (154)
64	EVA	ss3844142449	Apr 26, 2020 (154)
65	SGDP_PRJ	ss3866619573	Apr 26, 2020 (154)
66	KRGDB	ss3913645965	Apr 26, 2020 (154)
67	KOGIC	ss3960878132	Apr 26, 2020 (154)
68	TOPMED	ss4735400479	Apr 26, 2021 (155)
69	TOMMO_GENOMICS	ss5181791346	Apr 26, 2021 (155)
70	1000G_HIGH_COVERAGE	ss5271810214	Oct 14, 2022 (156)
71	EVA	ss5371617372	Oct 14, 2022 (156)
72	HUGCELL_USP	ss5469096100	Oct 14, 2022 (156)
73	EVA	ss5508845140	Oct 14, 2022 (156)
74	1000G_HIGH_COVERAGE	ss5559438733	Oct 14, 2022 (156)
75	SANFORD_IMAGENETICS	ss5642333622	Oct 14, 2022 (156)
76	TOMMO_GENOMICS	ss5721240692	Oct 14, 2022 (156)
77	YY_MCH	ss5808329954	Oct 14, 2022 (156)
78	EVA	ss5822402008	Oct 14, 2022 (156)
79	EVA	ss5855759897	Oct 14, 2022 (156)
80	EVA	ss5857684234	Oct 14, 2022 (156)
81	EVA	ss5971523613	Oct 14, 2022 (156)
82	1000Genomes	NC_000007.13 - 11602932	Oct 12, 2018 (152)
83	1000Genomes_30x	NC_000007.14 - 11563305	Oct 14, 2022 (156)
84	The Avon Longitudinal Study of Parents and Children	NC_000007.13 - 11602932	Oct 12, 2018 (152)
85	Genetic variation in the Estonian population	NC_000007.13 - 11602932	Oct 12, 2018 (152)
86	The Danish reference pan genome	NC_000007.13 - 11602932	Apr 26, 2020 (154)
87	gnomAD - Genomes Submission ignored due to conflicting rows: Row 252740676 (NC_000007.14:11563304:C:G 0/140162) Row 252740677 (NC_000007.14:11563304:C:T 117129/140144)	-	Apr 26, 2021 (155)
88	gnomAD - Genomes Submission ignored due to conflicting rows: Row 252740676 (NC_000007.14:11563304:C:G 0/140162) Row 252740677 (NC_000007.14:11563304:C:T 117129/140144)	-	Apr 26, 2021 (155)
89	Genome of the Netherlands Release 5	NC_000007.13 - 11602932	Apr 26, 2020 (154)
90	HapMap	NC_000007.14 - 11563305	Apr 26, 2020 (154)
91	KOREAN population from KRGDB	NC_000007.13 - 11602932	Apr 26, 2020 (154)
92	Korean Genome Project	NC_000007.14 - 11563305	Apr 26, 2020 (154)
93	Northern Sweden	NC_000007.13 - 11602932	Jul 13, 2019 (153)
94	Qatari	NC_000007.13 - 11602932	Apr 26, 2020 (154)
95	SGDP_PRJ	NC_000007.13 - 11602932	Apr 26, 2020 (154)
96	Siberian	NC_000007.13 - 11602932	Apr 26, 2020 (154)
97	8.3KJPN	NC_000007.13 - 11602932	Apr 26, 2021 (155)
98	14KJPN	NC_000007.14 - 11563305	Oct 14, 2022 (156)
99	TopMed	NC_000007.14 - 11563305	Apr 26, 2021 (155)
100	UK 10K study - Twins	NC_000007.13 - 11602932	Oct 12, 2018 (152)
101	A Vietnamese Genetic Variation Database	NC_000007.13 - 11602932	Jul 13, 2019 (153)
102	ALFA	NC_000007.14 - 11563305	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)
rs17635397	Mar 11, 2006 (126)
rs57929405	May 24, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
1511926027	NC_000007.14:11563304:C:G	NC_000007.14:11563304:C:G	(self)
ss77710812, ss85971399	NC_000007.11:11376171:C:T	NC_000007.14:11563304:C:T	(self)
ss93628225, ss111512494, ss113308224, ss115929889, ss162049890, ss163638259, ss166139891, ss202942977, ss208311583, ss254050076, ss279184054, ss285573985, ss293988670, ss1593507473	NC_000007.12:11569456:C:T	NC_000007.14:11563304:C:T	(self)
35835422, 19975547, 14276711, 8233309, 8901369, 20823359, 7638068, 9230544, 18636553, 4981085, 39760653, 19975547, 4446867, ss222903810, ss233847427, ss240827740, ss559802778, ss654151257, ss983943188, ss1074355641, ss1323908031, ss1431026827, ss1582068370, ss1617560461, ss1660554494, ss1804864987, ss1927188614, ss1970622824, ss2024265804, ss2152464731, ss2626622626, ss2708114976, ss2849707227, ss3000619748, ss3347434244, ss3668538463, ss3734353203, ss3766181574, ss3785732965, ss3791047224, ss3795926921, ss3830411382, ss3838691771, ss3866619573, ss3913645965, ss5181791346, ss5371617372, ss5508845140, ss5642333622, ss5822402008, ss5971523613	NC_000007.13:11602931:C:T	NC_000007.14:11563304:C:T	(self)
46964668, 3333553, 17256133, 55077796, 572778038, 1511926027, ss2291619741, ss3025926830, ss3648561387, ss3719091451, ss3809346912, ss3844142449, ss3960878132, ss4735400479, ss5271810214, ss5469096100, ss5559438733, ss5721240692, ss5808329954, ss5855759897, ss5857684234	NC_000007.14:11563304:C:T	NC_000007.14:11563304:C:T	(self)
ss10419258, ss11907538	NT_007819.13:10898604:C:T	NC_000007.14:11563304:C:T	(self)
ss17922011, ss22571149, ss22953051	NT_007819.14:10898604:C:T	NC_000007.14:11563304:C:T	(self)
ss14, ss24371965, ss98132681, ss105492517, ss139562268, ss142655515, ss158041781	NT_007819.17:11592931:C:T	NC_000007.14:11563304:C:T	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs15

PMID	Title	Author	Year	Journal
29936769	[Genetic variations in MLH3 and MSH2 genes are associated with the sensitivity and prognosis in locally advanced rectal cancer patients receiving preoperative chemoradiotherapy].	Yang J et al.	2018	Zhonghua zhong liu za zhi [Chinese journal of oncology]

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

rs15