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dbSNP Short Genetic Variations

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.

rs21

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr7:11557307 (GRCh38.p13) 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
G>A / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.387959 (102689/264690, TOPMED)
G=0.400259 (55941/139762, GnomAD)
G=0.42728 (20154/47168, ALFA) (+ 15 more)
G=0.41443 (6945/16758, 8.3KJPN)
G=0.3912 (1959/5008, 1000G)
G=0.4701 (2106/4480, Estonian)
G=0.4408 (1699/3854, ALSPAC)
G=0.4455 (1652/3708, TWINSUK)
G=0.4341 (1272/2930, KOREAN)
G=0.3487 (657/1884, HapMap)
G=0.4383 (803/1832, Korea1K)
A=0.476 (475/998, GoNL)
G=0.490 (294/600, NorthernSweden)
G=0.262 (118/450, SGDP_PRJ)
G=0.324 (70/216, Qatari)
G=0.416 (89/214, Vietnamese)
G=0.47 (19/40, GENOME_DK)
G=0.34 (13/38, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
THSD7A : Intron Variant
Publications
2 citations
Genomic View
See rs on genome
Help

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.p13 chr 7 NC_000007.14:g.11557307G>A
GRCh38.p13 chr 7 NC_000007.14:g.11557307G>C
GRCh37.p13 chr 7 NC_000007.13:g.11596934G>A
GRCh37.p13 chr 7 NC_000007.13:g.11596934G>C
THSD7A RefSeqGene NG_027670.1:g.279891C>T
THSD7A RefSeqGene NG_027670.1:g.279891C>G
Gene: THSD7A, thrombospondin type 1 domain containing 7A (minus strand)
Molecule type Change Amino acid[Codon] SO Term
THSD7A transcript NM_015204.3:c.1454-14190C…

NM_015204.3:c.1454-14190C>T

N/A Intron Variant
THSD7A transcript variant X1 XM_006715659.1:c.1454-141…

XM_006715659.1:c.1454-14190C>T

N/A Intron Variant
THSD7A transcript variant X4 XM_006715660.1:c.1454-141…

XM_006715660.1:c.1454-14190C>T

N/A Intron Variant
THSD7A transcript variant X6 XM_006715662.1:c.1454-141…

XM_006715662.1:c.1454-14190C>T

N/A Intron Variant
THSD7A transcript variant X2 XM_011515193.3:c.1247-141…

XM_011515193.3:c.1247-14190C>T

N/A Intron Variant
THSD7A transcript variant X3 XM_011515194.1:c.1247-141…

XM_011515194.1:c.1247-14190C>T

N/A Intron Variant
THSD7A transcript variant X5 XR_001744589.1:n. N/A Intron Variant
Help

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

ALFA Allele Frequency (New)
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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 47168 G=0.42728 A=0.57272
European Sub 33392 G=0.45870 A=0.54130
African Sub 5610 G=0.2795 A=0.7205
African Others Sub 192 G=0.224 A=0.776
African American Sub 5418 G=0.2815 A=0.7185
Asian Sub 486 G=0.405 A=0.595
East Asian Sub 388 G=0.420 A=0.580
Other Asian Sub 98 G=0.35 A=0.65
Latin American 1 Sub 660 G=0.370 A=0.630
Latin American 2 Sub 2976 G=0.3669 A=0.6331
South Asian Sub 174 G=0.443 A=0.557
Other Sub 3870 G=0.4287 A=0.5713


Help

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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 G=0.387959 A=0.612041
gnomAD - Genomes Global Study-wide 139762 G=0.400259 A=0.599741
gnomAD - Genomes European Sub 75708 G=0.46843 A=0.53157
gnomAD - Genomes African Sub 41890 G=0.29002 A=0.70998
gnomAD - Genomes American Sub 13586 G=0.34955 A=0.65045
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=0.4073 A=0.5927
gnomAD - Genomes East Asian Sub 3114 G=0.4342 A=0.5658
gnomAD - Genomes Other Sub 2142 G=0.4080 A=0.5920
8.3KJPN JAPANESE Study-wide 16758 G=0.41443 A=0.58557
1000Genomes Global Study-wide 5008 G=0.3912 A=0.6088
1000Genomes African Sub 1322 G=0.2496 A=0.7504
1000Genomes East Asian Sub 1008 G=0.4395 A=0.5605
1000Genomes Europe Sub 1006 G=0.4692 A=0.5308
1000Genomes South Asian Sub 978 G=0.491 A=0.509
1000Genomes American Sub 694 G=0.337 A=0.663
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.4701 A=0.5299
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.4408 A=0.5592
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.4455 A=0.5545
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.4341 A=0.5659, C=0.0000
HapMap Global Study-wide 1884 G=0.3487 A=0.6513
HapMap American Sub 766 G=0.426 A=0.574
HapMap African Sub 692 G=0.225 A=0.775
HapMap Asian Sub 250 G=0.396 A=0.604
HapMap Europe Sub 176 G=0.432 A=0.568
Korean Genome Project KOREAN Study-wide 1832 G=0.4383 A=0.5617
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.524 A=0.476
Northern Sweden ACPOP Study-wide 600 G=0.490 A=0.510
SGDP_PRJ Global Study-wide 450 G=0.262 A=0.738
Qatari Global Study-wide 216 G=0.324 A=0.676
A Vietnamese Genetic Variation Database Global Study-wide 214 G=0.416 A=0.584
The Danish reference pan genome Danish Study-wide 40 G=0.47 A=0.53
Siberian Global Study-wide 38 G=0.34 A=0.66
Help

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 G= A C
GRCh38.p13 chr 7 NC_000007.14:g.11557307= NC_000007.14:g.11557307G>A NC_000007.14:g.11557307G>C
GRCh37.p13 chr 7 NC_000007.13:g.11596934= NC_000007.13:g.11596934G>A NC_000007.13:g.11596934G>C
THSD7A RefSeqGene NG_027670.1:g.279891= NG_027670.1:g.279891C>T NG_027670.1:g.279891C>G
THSD7A transcript NM_015204.2:c.1454-14190= NM_015204.2:c.1454-14190C>T NM_015204.2:c.1454-14190C>G
THSD7A transcript NM_015204.3:c.1454-14190= NM_015204.3:c.1454-14190C>T NM_015204.3:c.1454-14190C>G
THSD7A transcript variant X1 XM_006715659.1:c.1454-14190= XM_006715659.1:c.1454-14190C>T XM_006715659.1:c.1454-14190C>G
THSD7A transcript variant X4 XM_006715660.1:c.1454-14190= XM_006715660.1:c.1454-14190C>T XM_006715660.1:c.1454-14190C>G
THSD7A transcript variant X6 XM_006715662.1:c.1454-14190= XM_006715662.1:c.1454-14190C>T XM_006715662.1:c.1454-14190C>G
THSD7A transcript variant X2 XM_011515193.3:c.1247-14190= XM_011515193.3:c.1247-14190C>T XM_011515193.3:c.1247-14190C>G
THSD7A transcript variant X3 XM_011515194.1:c.1247-14190= XM_011515194.1:c.1247-14190C>T XM_011515194.1:c.1247-14190C>G
Help

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#.

66 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss20 Sep 19, 2000 (36)
2 BCM_SSAHASNP ss10359613 Jul 11, 2003 (116)
3 WI_SSAHASNP ss11851752 Jul 11, 2003 (116)
4 PERLEGEN ss69004959 May 17, 2007 (127)
5 AFFY ss76506548 Dec 06, 2007 (129)
6 HGSV ss86039096 Dec 15, 2007 (130)
7 BCMHGSC_JDW ss93628200 Mar 24, 2008 (129)
8 BGI ss104398050 Dec 01, 2009 (131)
9 KRIBB_YJKIM ss104807665 Feb 05, 2009 (130)
10 1000GENOMES ss111512303 Jan 25, 2009 (130)
11 1000GENOMES ss113308068 Jan 25, 2009 (130)
12 ILLUMINA-UK ss115929820 Feb 14, 2009 (130)
13 ENSEMBL ss142655396 Dec 01, 2009 (131)
14 GMI ss158041628 Dec 01, 2009 (131)
15 ILLUMINA ss160501765 Dec 01, 2009 (131)
16 COMPLETE_GENOMICS ss163638103 Jul 04, 2010 (132)
17 COMPLETE_GENOMICS ss166139649 Jul 04, 2010 (132)
18 BUSHMAN ss202942835 Jul 04, 2010 (132)
19 1000GENOMES ss222903755 Jul 14, 2010 (132)
20 1000GENOMES ss233847376 Jul 15, 2010 (132)
21 1000GENOMES ss240827694 Jul 15, 2010 (132)
22 BL ss254049983 May 09, 2011 (134)
23 GMI ss279184003 May 04, 2012 (137)
24 GMI ss285573953 Apr 25, 2013 (138)
25 PJP ss293988655 May 09, 2011 (134)
26 ILLUMINA ss481221623 Sep 08, 2015 (146)
27 TISHKOFF ss559802725 Apr 25, 2013 (138)
28 SSMP ss654151203 Apr 25, 2013 (138)
29 EVA-GONL ss983943099 Aug 21, 2014 (142)
30 JMKIDD_LAB ss1074355580 Aug 21, 2014 (142)
31 1000GENOMES ss1323907823 Aug 21, 2014 (142)
32 DDI ss1431026799 Apr 01, 2015 (144)
33 EVA_GENOME_DK ss1582068323 Apr 01, 2015 (144)
34 EVA_DECODE ss1593507380 Apr 01, 2015 (144)
35 EVA_UK10K_ALSPAC ss1617560324 Apr 01, 2015 (144)
36 EVA_UK10K_TWINSUK ss1660554357 Apr 01, 2015 (144)
37 EVA_SVP ss1712930704 Apr 01, 2015 (144)
38 HAMMER_LAB ss1804864930 Sep 08, 2015 (146)
39 WEILL_CORNELL_DGM ss1927188533 Feb 12, 2016 (147)
40 GENOMED ss1970622789 Jul 19, 2016 (147)
41 JJLAB ss2024265739 Sep 14, 2016 (149)
42 USC_VALOUEV ss2152464679 Dec 20, 2016 (150)
43 HUMAN_LONGEVITY ss2291619286 Dec 20, 2016 (150)
44 TOPMED ss2460445421 Dec 20, 2016 (150)
45 SYSTEMSBIOZJU ss2626622587 Nov 08, 2017 (151)
46 GRF ss2708114926 Nov 08, 2017 (151)
47 GNOMAD ss2849706681 Nov 08, 2017 (151)
48 SWEGEN ss3000619632 Nov 08, 2017 (151)
49 BIOINF_KMB_FNS_UNIBA ss3025926796 Nov 08, 2017 (151)
50 CSHL ss3347434205 Nov 08, 2017 (151)
51 TOPMED ss3522359773 Nov 08, 2017 (151)
52 ILLUMINA ss3636837309 Oct 12, 2018 (152)
53 EGCUT_WGS ss3668538353 Jul 13, 2019 (153)
54 EVA_DECODE ss3719091322 Jul 13, 2019 (153)
55 ACPOP ss3734353119 Jul 13, 2019 (153)
56 EVA ss3766181495 Jul 13, 2019 (153)
57 PACBIO ss3785732922 Jul 13, 2019 (153)
58 PACBIO ss3791047184 Jul 13, 2019 (153)
59 PACBIO ss3795926881 Jul 13, 2019 (153)
60 KHV_HUMAN_GENOMES ss3809346821 Jul 13, 2019 (153)
61 EVA ss3830411323 Apr 26, 2020 (154)
62 SGDP_PRJ ss3866619444 Apr 26, 2020 (154)
63 KRGDB ss3913645847 Apr 26, 2020 (154)
64 KOGIC ss3960878041 Apr 26, 2020 (154)
65 TOPMED ss4735398595 Apr 26, 2021 (155)
66 TOMMO_GENOMICS ss5181791116 Apr 26, 2021 (155)
67 1000Genomes NC_000007.13 - 11596934 Oct 12, 2018 (152)
68 The Avon Longitudinal Study of Parents and Children NC_000007.13 - 11596934 Oct 12, 2018 (152)
69 Genetic variation in the Estonian population NC_000007.13 - 11596934 Oct 12, 2018 (152)
70 The Danish reference pan genome NC_000007.13 - 11596934 Apr 26, 2020 (154)
71 gnomAD - Genomes NC_000007.14 - 11557307 Apr 26, 2021 (155)
72 Genome of the Netherlands Release 5 NC_000007.13 - 11596934 Apr 26, 2020 (154)
73 HapMap NC_000007.14 - 11557307 Apr 26, 2020 (154)
74 KOREAN population from KRGDB NC_000007.13 - 11596934 Apr 26, 2020 (154)
75 Korean Genome Project NC_000007.14 - 11557307 Apr 26, 2020 (154)
76 Northern Sweden NC_000007.13 - 11596934 Jul 13, 2019 (153)
77 Qatari NC_000007.13 - 11596934 Apr 26, 2020 (154)
78 SGDP_PRJ NC_000007.13 - 11596934 Apr 26, 2020 (154)
79 Siberian NC_000007.13 - 11596934 Apr 26, 2020 (154)
80 8.3KJPN NC_000007.13 - 11596934 Apr 26, 2021 (155)
81 TopMed NC_000007.14 - 11557307 Apr 26, 2021 (155)
82 UK 10K study - Twins NC_000007.13 - 11596934 Oct 12, 2018 (152)
83 A Vietnamese Genetic Variation Database NC_000007.13 - 11596934 Jul 13, 2019 (153)
84 ALFA NC_000007.14 - 11557307 Apr 26, 2021 (155)
Help

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)
rs59048528 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss86039096 NC_000007.11:11370173:G:A NC_000007.14:11557306:G:A (self)
ss93628200, ss111512303, ss113308068, ss115929820, ss163638103, ss166139649, ss202942835, ss254049983, ss279184003, ss285573953, ss293988655, ss1593507380, ss1712930704 NC_000007.12:11563458:G:A NC_000007.14:11557306:G:A (self)
35835205, 19975395, 14276601, 8233262, 8901280, 20823241, 7637984, 9230463, 18636424, 4981033, 39760423, 19975395, 4446821, ss222903755, ss233847376, ss240827694, ss481221623, ss559802725, ss654151203, ss983943099, ss1074355580, ss1323907823, ss1431026799, ss1582068323, ss1617560324, ss1660554357, ss1804864930, ss1927188533, ss1970622789, ss2024265739, ss2152464679, ss2460445421, ss2626622587, ss2708114926, ss2849706681, ss3000619632, ss3347434205, ss3636837309, ss3668538353, ss3734353119, ss3766181495, ss3785732922, ss3791047184, ss3795926881, ss3830411323, ss3866619444, ss3913645847, ss5181791116 NC_000007.13:11596933:G:A NC_000007.14:11557306:G:A (self)
252739224, 3333519, 17256042, 358295087, 572776154, 15283743939, ss2291619286, ss3025926796, ss3522359773, ss3719091322, ss3809346821, ss3960878041, ss4735398595 NC_000007.14:11557306:G:A NC_000007.14:11557306:G:A (self)
ss10359613, ss11851752 NT_007819.13:10892606:G:A NC_000007.14:11557306:G:A (self)
ss20, ss69004959, ss76506548, ss104398050, ss104807665, ss142655396, ss158041628, ss160501765 NT_007819.17:11586933:G:A NC_000007.14:11557306:G:A (self)
20823241, ss3913645847 NC_000007.13:11596933:G:C NC_000007.14:11557306:G:C (self)
Help

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

2 citations for rs21
PMID Title Author Year Journal
19126244 Frequent loss of heterozygosity and altered expression of the candidate tumor suppressor gene 'FAT' in human astrocytic tumors. Chosdol K et al. 2009 BMC cancer
26739746 A multi-factorial analysis of response to warfarin in a UK prospective cohort. Bourgeois S et al. 2016 Genome medicine
Help

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.

Software version is: 2.0.1.post596+ae089ad