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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs975278

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr2:223982990 (GRCh38.p7) 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=0.24113 (30278/125568, TOPMED)
T=0.2341 (7244/30940, GnomAD)
T=0.321 (1607/5008, 1000G)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SERPINE2 : Intron Variant
Publications
12 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.p7 chr 2 NC_000002.12:g.223982990T>A
GRCh38.p7 chr 2 NC_000002.12:g.223982990T>C
GRCh37.p13 chr 2 NC_000002.11:g.224847707T>A
GRCh37.p13 chr 2 NC_000002.11:g.224847707T>C
SERPINE2 RefSeqGene NG_032907.1:g.61330A>T
SERPINE2 RefSeqGene NG_032907.1:g.61330A>G
Gene: SERPINE2, serpin family E member 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SERPINE2 transcript variant 2 NM_001136528.1:c. N/A Intron Variant
SERPINE2 transcript variant 4 NM_001136530.1:c. N/A Intron Variant
SERPINE2 transcript variant 1 NM_006216.3:c. N/A Intron Variant
SERPINE2 transcript variant 3 NR_073116.1:n. N/A Intron Variant
SERPINE2 transcript variant X1 XM_005246641.2:c. N/A Intron Variant
SERPINE2 transcript variant X2 XM_017004329.1:c. N/A Intron Variant
SERPINE2 transcript variant X2 XM_017004330.1:c. N/A Intron Variant
SERPINE2 transcript variant X4 XM_017004331.1:c. N/A Intron Variant
SERPINE2 transcript variant X5 XM_017004332.1:c. 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
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
Trans-Omics for Precision Medicine Global Study-wide 125568 T=0.24113 C=0.75887
The Genome Aggregation Database Global Study-wide 30940 T=0.2341 A=0.0001, C=0.7657
The Genome Aggregation Database European Sub 18492 T=0.1855 A=0.0001, C=0.8144
The Genome Aggregation Database African Sub 8710 T=0.283 A=0.000, C=0.717
The Genome Aggregation Database East Asian Sub 1618 T=0.562 A=0.001, C=0.438
The Genome Aggregation Database Other Sub 982 T=0.20 A=0.00, C=0.80
The Genome Aggregation Database American Sub 838 T=0.18 A=0.00, C=0.82
The Genome Aggregation Database Ashkenazi Jewish Sub 300 T=0.31 A=0.00, C=0.69
1000Genomes Global Study-wide 5008 T=0.321 C=0.679
1000Genomes African Sub 1322 T=0.293 C=0.707
1000Genomes East Asian Sub 1008 T=0.565 C=0.435
1000Genomes Europe Sub 1006 T=0.170 C=0.830
1000Genomes South Asian Sub 978 T=0.36 C=0.64
1000Genomes American Sub 694 T=0.18 C=0.82
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 T= A C Note
GRCh38.p7 chr 2 NC_000002.12:g.22...

NC_000002.12:g.223982990T=

NC_000002.12:g.22...

NC_000002.12:g.223982990T>A

NC_000002.12:g.22...

NC_000002.12:g.223982990T>C

GRCh37.p13 chr 2 NC_000002.11:g.22...

NC_000002.11:g.224847707T=

NC_000002.11:g.22...

NC_000002.11:g.224847707T>A

NC_000002.11:g.22...

NC_000002.11:g.224847707T>C

SERPINE2 RefSeqGene NG_032907.1:g.613...

NG_032907.1:g.61330A=

NG_032907.1:g.613...

NG_032907.1:g.61330A>T

NG_032907.1:g.613...

NG_032907.1:g.61330A>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#.

3 Frequency, 107 SubSNP submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss1426638 Oct 05, 2000 (86)
2 SC_JCM ss6025324 Feb 20, 2003 (111)
3 WUGSC_SSAHASNP ss14470361 Dec 05, 2003 (119)
4 CSHL-HAPMAP ss16814972 Feb 27, 2004 (120)
5 SSAHASNP ss21584878 Apr 05, 2004 (121)
6 PERLEGEN ss23901127 Sep 20, 2004 (123)
7 ABI ss44184874 Mar 13, 2006 (126)
8 ILLUMINA ss65757478 Oct 16, 2006 (127)
9 ILLUMINA ss66663527 Dec 02, 2006 (127)
10 ILLUMINA ss67944109 Dec 02, 2006 (127)
11 ILLUMINA ss68058819 Dec 02, 2006 (127)
12 PERLEGEN ss68844604 May 18, 2007 (127)
13 ILLUMINA ss71623594 May 18, 2007 (127)
14 ILLUMINA ss75539608 Dec 07, 2007 (129)
15 HGSV ss77189681 Dec 07, 2007 (129)
16 ILLUMINA ss79303674 Dec 15, 2007 (130)
17 HGSV ss81223627 Dec 15, 2007 (130)
18 KRIBB_YJKIM ss83639641 Dec 15, 2007 (130)
19 BCMHGSC_JDW ss91565836 Mar 24, 2008 (129)
20 HUMANGENOME_JCVI ss96476307 Feb 04, 2009 (130)
21 ILLUMINA ss98285900 May 24, 2008 (130)
22 BGI ss106164545 Feb 04, 2009 (130)
23 1000GENOMES ss110844615 Jan 25, 2009 (130)
24 1000GENOMES ss111727643 Jan 25, 2009 (130)
25 ILLUMINA-UK ss118097419 Feb 14, 2009 (130)
26 ILLUMINA ss123035529 Dec 01, 2009 (131)
27 ENSEMBL ss135953509 Dec 01, 2009 (131)
28 ENSEMBL ss138639710 Dec 01, 2009 (131)
29 ILLUMINA ss154508229 Dec 01, 2009 (131)
30 GMI ss154778444 Dec 01, 2009 (131)
31 ILLUMINA ss159682183 Dec 01, 2009 (131)
32 ILLUMINA ss161010371 Dec 01, 2009 (131)
33 COMPLETE_GENOMICS ss165579811 Jul 04, 2010 (132)
34 COMPLETE_GENOMICS ss165932314 Jul 04, 2010 (132)
35 COMPLETE_GENOMICS ss167588122 Jul 04, 2010 (132)
36 ILLUMINA ss172497294 Jul 04, 2010 (132)
37 ILLUMINA ss174893137 Jul 04, 2010 (132)
38 BUSHMAN ss201804614 Jul 04, 2010 (132)
39 BCM-HGSC-SUB ss205753878 Jul 04, 2010 (132)
40 1000GENOMES ss219841862 Jul 14, 2010 (132)
41 1000GENOMES ss231606616 Jul 14, 2010 (132)
42 1000GENOMES ss239061089 Jul 15, 2010 (132)
43 BL ss253902509 May 09, 2011 (134)
44 GMI ss276917119 May 04, 2012 (137)
45 GMI ss284550902 Apr 25, 2013 (138)
46 PJP ss292497808 May 09, 2011 (134)
47 ILLUMINA ss481971567 May 04, 2012 (137)
48 ILLUMINA ss482005319 May 04, 2012 (137)
49 ILLUMINA ss482959199 Sep 08, 2015 (146)
50 ILLUMINA ss485779265 May 04, 2012 (137)
51 ILLUMINA ss537625405 Sep 08, 2015 (146)
52 TISHKOFF ss556256200 Apr 25, 2013 (138)
53 SSMP ss649919827 Apr 25, 2013 (138)
54 ILLUMINA ss778646595 Sep 08, 2015 (146)
55 ILLUMINA ss783335506 Sep 08, 2015 (146)
56 ILLUMINA ss784287091 Sep 08, 2015 (146)
57 ILLUMINA ss825634192 Apr 01, 2015 (144)
58 ILLUMINA ss832597334 Sep 08, 2015 (146)
59 ILLUMINA ss834104358 Sep 08, 2015 (146)
60 EVA-GONL ss978013644 Aug 21, 2014 (142)
61 JMKIDD_LAB ss1069980950 Aug 21, 2014 (142)
62 1000GENOMES ss1301851702 Aug 21, 2014 (142)
63 DDI ss1428927128 Apr 01, 2015 (144)
64 EVA_GENOME_DK ss1579344101 Apr 01, 2015 (144)
65 EVA_DECODE ss1587470704 Apr 01, 2015 (144)
66 EVA_DECODE ss1587470705 Apr 01, 2015 (144)
67 EVA_UK10K_ALSPAC ss1605905061 Apr 01, 2015 (144)
68 EVA_UK10K_ALSPAC ss1605905062 Apr 01, 2015 (144)
69 EVA_UK10K_TWINSUK ss1648899094 Apr 01, 2015 (144)
70 EVA_UK10K_TWINSUK ss1648899095 Apr 01, 2015 (144)
71 EVA_SVP ss1712534804 Apr 01, 2015 (144)
72 ILLUMINA ss1752341565 Sep 08, 2015 (146)
73 HAMMER_LAB ss1798444915 Sep 08, 2015 (146)
74 WEILL_CORNELL_DGM ss1921259303 Feb 12, 2016 (147)
75 ILLUMINA ss1946068030 Feb 12, 2016 (147)
76 ILLUMINA ss1958510705 Feb 12, 2016 (147)
77 GENOMED ss1969038379 Jul 19, 2016 (147)
78 JJLAB ss2021177869 Sep 14, 2016 (149)
79 USC_VALOUEV ss2149241824 Dec 20, 2016 (150)
80 HUMAN_LONGEVITY ss2239583843 Dec 20, 2016 (150)
81 TOPMED ss2406040947 Dec 20, 2016 (150)
82 SYSTEMSBIOZJU ss2625089238 Nov 08, 2017 (151)
83 ILLUMINA ss2633746446 Nov 08, 2017 (151)
84 GRF ss2703891339 Nov 08, 2017 (151)
85 ILLUMINA ss2710927351 Nov 08, 2017 (151)
86 GNOMAD ss2786911203 Nov 08, 2017 (151)
87 SWEGEN ss2991441017 Nov 08, 2017 (151)
88 ILLUMINA ss3022075279 Nov 08, 2017 (151)
89 BIOINF_KMB_FNS_UNIBA ss3024347528 Nov 08, 2017 (151)
90 TOPMED ss3339738618 Nov 08, 2017 (151)
91 TOPMED ss3339738619 Nov 08, 2017 (151)
92 CSHL ss3344764083 Nov 08, 2017 (151)
93 ILLUMINA ss3625777598 Jul 19, 2018 (151)
94 ILLUMINA ss3628298529 Jul 19, 2018 (151)
95 ILLUMINA ss3631706070 Jul 19, 2018 (151)
96 ILLUMINA ss3633236163 Jul 19, 2018 (151)
97 ILLUMINA ss3633949425 Jul 19, 2018 (151)
98 ILLUMINA ss3634814833 Jul 19, 2018 (151)
99 ILLUMINA ss3635634826 Jul 19, 2018 (151)
100 ILLUMINA ss3636504669 Jul 19, 2018 (151)
101 ILLUMINA ss3637386853 Jul 19, 2018 (151)
102 ILLUMINA ss3638321722 Jul 19, 2018 (151)
103 ILLUMINA ss3639164147 Jul 19, 2018 (151)
104 ILLUMINA ss3639595600 Jul 19, 2018 (151)
105 ILLUMINA ss3640522132 Jul 19, 2018 (151)
106 ILLUMINA ss3643286133 Jul 19, 2018 (151)
107 ILLUMINA ss3644770712 Jul 19, 2018 (151)
108 1000Genomes NC_000002.11 - 224847707 Jul 19, 2018 (151)
109 The Genome Aggregation Database NC_000002.11 - 224847707 Jul 19, 2018 (151)
110 Trans-Omics for Precision Medicine NC_000002.12 - 223982990 Jul 19, 2018 (151)
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)
rs58218914 May 24, 2008 (130)
rs386624666 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss77189681, ss81223627, ss3639164147, ss3639595600 NC_000002.9:224673211:T= NC_000002.12:223982989:T= (self)
ss91565836, ss110844615, ss111727643, ss118097419, ss161010371, ss165579811, ss165932314, ss167588122, ss201804614, ss205753878, ss253902509, ss276917119, ss284550902, ss292497808, ss481971567, ss825634192, ss1587470704, ss1587470705, ss1712534804, ss3643286133 NC_000002.10:224555950:T= NC_000002.12:223982989:T= (self)
12964405, 116401064, ss219841862, ss231606616, ss239061089, ss482005319, ss482959199, ss485779265, ss537625405, ss556256200, ss649919827, ss778646595, ss783335506, ss784287091, ss832597334, ss834104358, ss978013644, ss1069980950, ss1301851702, ss1428927128, ss1579344101, ss1605905061, ss1605905062, ss1648899094, ss1648899095, ss1752341565, ss1798444915, ss1921259303, ss1946068030, ss1958510705, ss1969038379, ss2021177869, ss2149241824, ss2406040947, ss2625089238, ss2633746446, ss2703891339, ss2710927351, ss2786911203, ss2991441017, ss3022075279, ss3344764083, ss3625777598, ss3628298529, ss3631706070, ss3633236163, ss3633949425, ss3634814833, ss3635634826, ss3636504669, ss3637386853, ss3638321722, ss3640522132, ss3644770712 NC_000002.11:224847706:T= NC_000002.12:223982989:T= (self)
218641334, ss2239583843, ss3024347528, ss3339738618, ss3339738619 NC_000002.12:223982989:T= NC_000002.12:223982989:T= (self)
ss14470361, ss16814972, ss21584878 NT_005403.14:75057118:T= NC_000002.12:223982989:T= (self)
ss1426638, ss6025324, ss23901127, ss44184874, ss65757478, ss66663527, ss67944109, ss68058819, ss68844604, ss71623594, ss75539608, ss79303674, ss83639641, ss96476307, ss98285900, ss106164545, ss123035529, ss135953509, ss138639710, ss154508229, ss154778444, ss159682183, ss172497294, ss174893137 NT_005403.17:75057124:T= NC_000002.12:223982989:T= (self)
ss1587470704 NC_000002.10:224555950:T>A NC_000002.12:223982989:T>A (self)
116401064, ss1605905062, ss1648899095, ss2786911203 NC_000002.11:224847706:T>A NC_000002.12:223982989:T>A (self)
ss2239583843, ss3339738618 NC_000002.12:223982989:T>A NC_000002.12:223982989:T>A (self)
ss77189681, ss81223627, ss3639164147, ss3639595600 NC_000002.9:224673211:T>C NC_000002.12:223982989:T>C (self)
ss91565836, ss110844615, ss111727643, ss118097419, ss161010371, ss165579811, ss165932314, ss167588122, ss201804614, ss205753878, ss253902509, ss276917119, ss284550902, ss292497808, ss481971567, ss825634192, ss1587470705, ss1712534804, ss3643286133 NC_000002.10:224555950:T>C NC_000002.12:223982989:T>C (self)
12964405, 116401064, ss219841862, ss231606616, ss239061089, ss482005319, ss482959199, ss485779265, ss537625405, ss556256200, ss649919827, ss778646595, ss783335506, ss784287091, ss832597334, ss834104358, ss978013644, ss1069980950, ss1301851702, ss1428927128, ss1579344101, ss1605905061, ss1648899094, ss1752341565, ss1798444915, ss1921259303, ss1946068030, ss1958510705, ss1969038379, ss2021177869, ss2149241824, ss2406040947, ss2625089238, ss2633746446, ss2703891339, ss2710927351, ss2786911203, ss2991441017, ss3022075279, ss3344764083, ss3625777598, ss3628298529, ss3631706070, ss3633236163, ss3633949425, ss3634814833, ss3635634826, ss3636504669, ss3637386853, ss3638321722, ss3640522132, ss3644770712 NC_000002.11:224847706:T>C NC_000002.12:223982989:T>C (self)
218641334, ss2239583843, ss3024347528, ss3339738619 NC_000002.12:223982989:T>C NC_000002.12:223982989:T>C (self)
ss14470361, ss16814972, ss21584878 NT_005403.14:75057118:T>C NC_000002.12:223982989:T>C (self)
ss1426638, ss6025324, ss23901127, ss44184874, ss65757478, ss66663527, ss67944109, ss68058819, ss68844604, ss71623594, ss75539608, ss79303674, ss83639641, ss96476307, ss98285900, ss106164545, ss123035529, ss135953509, ss138639710, ss154508229, ss154778444, ss159682183, ss172497294, ss174893137 NT_005403.17:75057124:T>C NC_000002.12:223982989:T>C (self)
Help

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

12 citations for rs975278
PMID Title Author Year Journal
16358219 The SERPINE2 gene is associated with chronic obstructive pulmonary disease. Demeo DL et al. 2006 American journal of human genetics
17363767 Genetic determinants of emphysema distribution in the national emphysema treatment trial. DeMeo DL et al. 2007 American journal of respiratory and critical care medicine
19017876 Genetic associations with hypoxemia and pulmonary arterial pressure in COPD. Castaldi PJ et al. 2009 Chest
19949669 SERPINE2 polymorphisms and chronic obstructive pulmonary disease. Cha SI et al. 2009 Journal of Korean medical science
20233420 Cluster analysis in severe emphysema subjects using phenotype and genotype data: an exploratory investigation. Cho MH et al. 2010 Respiratory research
20525719 Association of COPD candidate genes with computed tomography emphysema and airway phenotypes in severe COPD. Kim WJ et al. 2011 The European respiratory journal
21067581 Polymorphism of SERPINE2 gene is associated with pulmonary emphysema in consecutive autopsy cases. Fujimoto K et al. 2010 BMC medical genetics
21401569 Combining disease models to test for gene-environment interaction in nuclear families. Hoffmann TJ et al. 2011 Biometrics
21436250 Association of SERPINE2 with asthma. Himes BE et al. 2011 Chest
21611750 Association of SERPINE2 gene with the risk of chronic obstructive pulmonary disease and spirometric phenotypes in northern Han Chinese population. An L et al. 2012 Molecular biology reports
22145704 SERPINE2 haplotype as a risk factor for panlobular type of emphysema. Kukkonen MK et al. 2011 BMC medical genetics
27193053 Exploring the interaction among EPHX1, GSTP1, SERPINE2, and TGFB1 contributing to the quantitative traits of chronic obstructive pulmonary disease in Chinese Han population. An L et al. 2016 Human genomics

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: 0.1.4.post833+d3ba21e