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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.

rs71

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr7:11565881 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.234814 (62153/264690, TOPMED)
A=0.224636 (31458/140040, GnomAD)
A=0.25472 (6093/23920, ALFA) (+ 15 more)
A=0.24872 (4168/16758, 8.3KJPN)
A=0.2001 (1002/5008, 1000G)
A=0.2404 (1077/4480, Estonian)
A=0.2636 (1016/3854, ALSPAC)
A=0.2570 (953/3708, TWINSUK)
A=0.2290 (671/2930, KOREAN)
A=0.1938 (329/1698, HapMap)
A=0.230 (230/998, GoNL)
A=0.463 (290/626, Chileans)
A=0.227 (136/600, NorthernSweden)
A=0.231 (50/216, Qatari)
A=0.168 (36/214, Vietnamese)
G=0.402 (74/184, SGDP_PRJ)
A=0.28 (11/40, GENOME_DK)
G=0.36 (5/14, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
THSD7A : Intron Variant
LOC105375151 : Non Coding Transcript Variant
Publications
0 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.11565881G>A
GRCh37.p13 chr 7 NC_000007.13:g.11605508G>A
THSD7A RefSeqGene NG_027670.1:g.271317C>T
Gene: THSD7A, thrombospondin type 1 domain containing 7A (minus strand)
Molecule type Change Amino acid[Codon] SO Term
THSD7A transcript NM_015204.3:c.1454-22764C…

NM_015204.3:c.1454-22764C>T

N/A Intron Variant
THSD7A transcript variant X1 XM_006715659.1:c.1454-227…

XM_006715659.1:c.1454-22764C>T

N/A Intron Variant
THSD7A transcript variant X4 XM_006715660.1:c.1454-227…

XM_006715660.1:c.1454-22764C>T

N/A Intron Variant
THSD7A transcript variant X6 XM_006715662.1:c.1454-227…

XM_006715662.1:c.1454-22764C>T

N/A Intron Variant
THSD7A transcript variant X2 XM_011515193.3:c.1247-227…

XM_011515193.3:c.1247-22764C>T

N/A Intron Variant
THSD7A transcript variant X3 XM_011515194.1:c.1247-227…

XM_011515194.1:c.1247-22764C>T

N/A Intron Variant
THSD7A transcript variant X5 XR_001744589.1:n. N/A Intron Variant
Gene: LOC105375151, uncharacterized LOC105375151 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC105375151 transcript variant X2 XR_001744905.2:n.323G>A N/A Non Coding Transcript Variant
LOC105375151 transcript variant X1 XR_001744904.1:n. N/A Genic Upstream Transcript 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
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 23920 G=0.74528 A=0.25472
European Sub 15652 G=0.74419 A=0.25581
African Sub 3618 G=0.8889 A=0.1111
African Others Sub 126 G=0.960 A=0.040
African American Sub 3492 G=0.8863 A=0.1137
Asian Sub 160 G=0.812 A=0.188
East Asian Sub 102 G=0.804 A=0.196
Other Asian Sub 58 G=0.83 A=0.17
Latin American 1 Sub 292 G=0.733 A=0.267
Latin American 2 Sub 2748 G=0.5757 A=0.4243
South Asian Sub 110 G=0.891 A=0.109
Other Sub 1340 G=0.7007 A=0.2993


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=0.765186 A=0.234814
gnomAD - Genomes Global Study-wide 140040 G=0.775364 A=0.224636
gnomAD - Genomes European Sub 75838 G=0.75167 A=0.24833
gnomAD - Genomes African Sub 41966 G=0.88350 A=0.11650
gnomAD - Genomes American Sub 13636 G=0.59204 A=0.40796
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=0.6830 A=0.3170
gnomAD - Genomes East Asian Sub 3126 G=0.8077 A=0.1923
gnomAD - Genomes Other Sub 2152 G=0.7588 A=0.2412
8.3KJPN JAPANESE Study-wide 16758 G=0.75128 A=0.24872
1000Genomes Global Study-wide 5008 G=0.7999 A=0.2001
1000Genomes African Sub 1322 G=0.9039 A=0.0961
1000Genomes East Asian Sub 1008 G=0.8075 A=0.1925
1000Genomes Europe Sub 1006 G=0.7505 A=0.2495
1000Genomes South Asian Sub 978 G=0.845 A=0.155
1000Genomes American Sub 694 G=0.599 A=0.401
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.7596 A=0.2404
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.7364 A=0.2636
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.7430 A=0.2570
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.7710 A=0.2290
HapMap Global Study-wide 1698 G=0.8062 A=0.1938
HapMap American Sub 760 G=0.761 A=0.239
HapMap African Sub 684 G=0.877 A=0.123
HapMap Asian Sub 254 G=0.752 A=0.248
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.770 A=0.230
Chileans Chilean Study-wide 626 G=0.537 A=0.463
Northern Sweden ACPOP Study-wide 600 G=0.773 A=0.227
Qatari Global Study-wide 216 G=0.769 A=0.231
A Vietnamese Genetic Variation Database Global Study-wide 214 G=0.832 A=0.168
SGDP_PRJ Global Study-wide 184 G=0.402 A=0.598
The Danish reference pan genome Danish Study-wide 40 G=0.72 A=0.28
Siberian Global Study-wide 14 G=0.36 A=0.64
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
GRCh38.p13 chr 7 NC_000007.14:g.11565881= NC_000007.14:g.11565881G>A
GRCh37.p13 chr 7 NC_000007.13:g.11605508= NC_000007.13:g.11605508G>A
THSD7A RefSeqGene NG_027670.1:g.271317= NG_027670.1:g.271317C>T
LOC105375151 transcript variant X2 XR_001744905.2:n.323= XR_001744905.2:n.323G>A
THSD7A transcript NM_015204.2:c.1454-22764= NM_015204.2:c.1454-22764C>T
THSD7A transcript NM_015204.3:c.1454-22764= NM_015204.3:c.1454-22764C>T
THSD7A transcript variant X1 XM_006715659.1:c.1454-22764= XM_006715659.1:c.1454-22764C>T
THSD7A transcript variant X4 XM_006715660.1:c.1454-22764= XM_006715660.1:c.1454-22764C>T
THSD7A transcript variant X6 XM_006715662.1:c.1454-22764= XM_006715662.1:c.1454-22764C>T
THSD7A transcript variant X2 XM_011515193.3:c.1247-22764= XM_011515193.3:c.1247-22764C>T
THSD7A transcript variant X3 XM_011515194.1:c.1247-22764= XM_011515194.1:c.1247-22764C>T
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#.

50 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss70 Sep 19, 2000 (36)
2 CSHL-HAPMAP ss19722646 Feb 27, 2004 (120)
3 ABI ss44832983 Mar 13, 2006 (126)
4 AFFY ss76704818 Dec 07, 2007 (129)
5 KRIBB_YJKIM ss104807666 Feb 05, 2009 (130)
6 GMI ss158041862 Dec 01, 2009 (131)
7 COMPLETE_GENOMICS ss166140044 Jul 04, 2010 (132)
8 BUSHMAN ss202943059 Jul 04, 2010 (132)
9 1000GENOMES ss222903844 Jul 14, 2010 (132)
10 1000GENOMES ss233847453 Jul 15, 2010 (132)
11 1000GENOMES ss240827765 Jul 15, 2010 (132)
12 BL ss254050157 May 09, 2011 (134)
13 GMI ss279184083 May 04, 2012 (137)
14 GMI ss285574003 Apr 25, 2013 (138)
15 TISHKOFF ss559802817 Apr 25, 2013 (138)
16 SSMP ss654151289 Apr 25, 2013 (138)
17 EVA-GONL ss983943232 Aug 21, 2014 (142)
18 JMKIDD_LAB ss1074355684 Aug 21, 2014 (142)
19 1000GENOMES ss1323908152 Aug 21, 2014 (142)
20 EVA_GENOME_DK ss1582068393 Apr 01, 2015 (144)
21 EVA_DECODE ss1593507525 Apr 01, 2015 (144)
22 EVA_UK10K_ALSPAC ss1617560542 Apr 01, 2015 (144)
23 EVA_UK10K_TWINSUK ss1660554575 Apr 01, 2015 (144)
24 EVA_SVP ss1712930718 Apr 01, 2015 (144)
25 HAMMER_LAB ss1804865014 Sep 08, 2015 (146)
26 WEILL_CORNELL_DGM ss1927188650 Feb 12, 2016 (147)
27 GENOMED ss1970622842 Jul 19, 2016 (147)
28 JJLAB ss2024265837 Sep 14, 2016 (149)
29 USC_VALOUEV ss2152464762 Dec 20, 2016 (150)
30 HUMAN_LONGEVITY ss2291619974 Dec 20, 2016 (150)
31 TOPMED ss2460446129 Dec 20, 2016 (150)
32 GRF ss2708115008 Nov 08, 2017 (151)
33 GNOMAD ss2849707501 Nov 08, 2017 (151)
34 SWEGEN ss3000619811 Nov 08, 2017 (151)
35 BIOINF_KMB_FNS_UNIBA ss3025926851 Nov 08, 2017 (151)
36 CSHL ss3347434268 Nov 08, 2017 (151)
37 TOPMED ss3522361737 Nov 08, 2017 (151)
38 EGCUT_WGS ss3668538534 Jul 13, 2019 (153)
39 EVA_DECODE ss3719091517 Jul 13, 2019 (153)
40 ACPOP ss3734353247 Jul 13, 2019 (153)
41 EVA ss3766181624 Jul 13, 2019 (153)
42 PACBIO ss3785732984 Jul 13, 2019 (153)
43 PACBIO ss3791047243 Jul 13, 2019 (153)
44 PACBIO ss3795926940 Jul 13, 2019 (153)
45 KHV_HUMAN_GENOMES ss3809346958 Jul 13, 2019 (153)
46 EVA ss3830411406 Apr 26, 2020 (154)
47 SGDP_PRJ ss3866619635 Apr 26, 2020 (154)
48 KRGDB ss3913646025 Apr 26, 2020 (154)
49 TOPMED ss4735401360 Apr 26, 2021 (155)
50 TOMMO_GENOMICS ss5181791468 Apr 26, 2021 (155)
51 1000Genomes NC_000007.13 - 11605508 Oct 12, 2018 (152)
52 The Avon Longitudinal Study of Parents and Children NC_000007.13 - 11605508 Oct 12, 2018 (152)
53 Chileans NC_000007.13 - 11605508 Apr 26, 2020 (154)
54 Genetic variation in the Estonian population NC_000007.13 - 11605508 Oct 12, 2018 (152)
55 The Danish reference pan genome NC_000007.13 - 11605508 Apr 26, 2020 (154)
56 gnomAD - Genomes NC_000007.14 - 11565881 Apr 26, 2021 (155)
57 Genome of the Netherlands Release 5 NC_000007.13 - 11605508 Apr 26, 2020 (154)
58 HapMap NC_000007.14 - 11565881 Apr 26, 2020 (154)
59 KOREAN population from KRGDB NC_000007.13 - 11605508 Apr 26, 2020 (154)
60 Northern Sweden NC_000007.13 - 11605508 Jul 13, 2019 (153)
61 Qatari NC_000007.13 - 11605508 Apr 26, 2020 (154)
62 SGDP_PRJ NC_000007.13 - 11605508 Apr 26, 2020 (154)
63 Siberian NC_000007.13 - 11605508 Apr 26, 2020 (154)
64 8.3KJPN NC_000007.13 - 11605508 Apr 26, 2021 (155)
65 TopMed NC_000007.14 - 11565881 Apr 26, 2021 (155)
66 UK 10K study - Twins NC_000007.13 - 11605508 Oct 12, 2018 (152)
67 A Vietnamese Genetic Variation Database NC_000007.13 - 11605508 Jul 13, 2019 (153)
68 ALFA NC_000007.14 - 11565881 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss166140044, ss202943059, ss254050157, ss279184083, ss285574003, ss1593507525, ss1712930718 NC_000007.12:11572032:G:A NC_000007.14:11565880:G:A (self)
35835546, 19975630, 401027, 14276782, 8233332, 8901413, 20823419, 7638112, 9230580, 18636615, 4981116, 39760775, 19975630, 4446894, ss222903844, ss233847453, ss240827765, ss559802817, ss654151289, ss983943232, ss1074355684, ss1323908152, ss1582068393, ss1617560542, ss1660554575, ss1804865014, ss1927188650, ss1970622842, ss2024265837, ss2152464762, ss2460446129, ss2708115008, ss2849707501, ss3000619811, ss3347434268, ss3668538534, ss3734353247, ss3766181624, ss3785732984, ss3791047243, ss3795926940, ss3830411406, ss3866619635, ss3913646025, ss5181791468 NC_000007.13:11605507:G:A NC_000007.14:11565880:G:A (self)
252741356, 3333574, 358296829, 572778919, 14268490232, ss2291619974, ss3025926851, ss3522361737, ss3719091517, ss3809346958, ss4735401360 NC_000007.14:11565880:G:A NC_000007.14:11565880:G:A (self)
ss19722646 NT_007819.14:10901180:G:A NC_000007.14:11565880:G:A (self)
ss70, ss44832983, ss76704818, ss104807666, ss158041862 NT_007819.17:11595507:G:A NC_000007.14:11565880:G:A (self)
Help

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

No publications for rs71

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