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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 Aliases 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.

rs3790126

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr16:10530692 (GRCh38.p12) 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
T=0.11263 (14143/125568, TOPMED)
T=0.1226 (9651/78698, PAGE_STUDY)
T=0.174 (871/5008, 1000G) (+ 5 more)
T=0.099 (443/4480, Estonian)
T=0.087 (337/3854, ALSPAC)
T=0.084 (312/3708, TWINSUK)
T=0.11 (64/600, NorthernSweden)
T=0.14 (29/214, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
EMP2 : 3 Prime UTR 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.p12 chr 16 NC_000016.10:g.10530692C>G
GRCh38.p12 chr 16 NC_000016.10:g.10530692C>T
GRCh37.p13 chr 16 NC_000016.9:g.10624549C>G
GRCh37.p13 chr 16 NC_000016.9:g.10624549C>T
EMP2 RefSeqGene NG_042058.1:g.55025G>C
EMP2 RefSeqGene NG_042058.1:g.55025G>A
Gene: EMP2, epithelial membrane protein 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
EMP2 transcript NM_001424.6:c.*2213= N/A 3 Prime UTR Variant
EMP2 transcript variant X1 XM_006720864.3:c.*2213= N/A 3 Prime UTR 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
TopMed Global Study-wide 125568 C=0.88737 T=0.11263
The PAGE Study Global Study-wide 78698 C=0.8774 T=0.1226
The PAGE Study AfricanAmerican Sub 32514 C=0.8588 T=0.1412
The PAGE Study Mexican Sub 10810 C=0.9484 T=0.0516
The PAGE Study Asian Sub 8318 C=0.791 T=0.209
The PAGE Study PuertoRican Sub 7916 C=0.904 T=0.096
The PAGE Study NativeHawaiian Sub 4534 C=0.879 T=0.121
The PAGE Study Cuban Sub 4230 C=0.915 T=0.085
The PAGE Study Dominican Sub 3828 C=0.880 T=0.120
The PAGE Study CentralAmerican Sub 2450 C=0.936 T=0.064
The PAGE Study SouthAmerican Sub 1982 C=0.948 T=0.052
The PAGE Study NativeAmerican Sub 1260 C=0.919 T=0.081
The PAGE Study SouthAsian Sub 856 C=0.68 T=0.32
1000Genomes Global Study-wide 5008 C=0.826 T=0.174
1000Genomes African Sub 1322 C=0.822 T=0.178
1000Genomes East Asian Sub 1008 C=0.828 T=0.172
1000Genomes Europe Sub 1006 C=0.918 T=0.082
1000Genomes South Asian Sub 978 C=0.65 T=0.35
1000Genomes American Sub 694 C=0.94 T=0.06
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.901 T=0.099
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.913 T=0.087
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.916 T=0.084
Northern Sweden ACPOP Study-wide 600 C=0.89 T=0.11
A Vietnamese Genetic Variation Database Global Study-wide 214 C=0.86 T=0.14
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 C= G T Note
GRCh38.p12 chr 16 NC_000016.10:g.10...

NC_000016.10:g.10530692=

NC_000016.10:g.10...

NC_000016.10:g.10530692C>G

NC_000016.10:g.10...

NC_000016.10:g.10530692C>T

GRCh37.p13 chr 16 NC_000016.9:g.106...

NC_000016.9:g.10624549=

NC_000016.9:g.106...

NC_000016.9:g.10624549C>G

NC_000016.9:g.106...

NC_000016.9:g.10624549C>T

EMP2 RefSeqGene NG_042058.1:g.55025= NG_042058.1:g.550...

NG_042058.1:g.55025G>C

NG_042058.1:g.550...

NG_042058.1:g.55025G>A

EMP2 transcript NM_001424.5:c.*2213= NM_001424.5:c.*22...

NM_001424.5:c.*2213G>C

NM_001424.5:c.*22...

NM_001424.5:c.*2213G>A

EMP2 transcript NM_001424.6:c.*2213= NM_001424.6:c.*22...

NM_001424.6:c.*2213G>C

NM_001424.6:c.*22...

NM_001424.6:c.*2213G>A

EMP2 transcript NM_001424.4:c.*2213= NM_001424.4:c.*22...

NM_001424.4:c.*2213G>C

NM_001424.4:c.*22...

NM_001424.4:c.*2213G>A

EMP2 transcript variant X1 XM_006720864.3:c....

XM_006720864.3:c.*2213=

XM_006720864.3:c....

XM_006720864.3:c.*2213G>C

XM_006720864.3:c....

XM_006720864.3:c.*2213G>A

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#.

104 SubSNP, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 YUSUKE ss4976496 Aug 28, 2002 (107)
2 BCM_SSAHASNP ss10804094 Jul 11, 2003 (116)
3 AFFY ss66213101 Nov 29, 2006 (127)
4 ILLUMINA ss66681750 Nov 29, 2006 (127)
5 ILLUMINA ss67303443 Nov 29, 2006 (127)
6 ILLUMINA ss67708420 Nov 29, 2006 (127)
7 PERLEGEN ss69339050 May 16, 2007 (127)
8 ILLUMINA ss70782094 May 23, 2008 (130)
9 ILLUMINA ss71358608 May 16, 2007 (127)
10 ILLUMINA ss75606524 Dec 06, 2007 (129)
11 AFFY ss76359580 Dec 06, 2007 (129)
12 ILLUMINA ss79167542 Dec 14, 2007 (130)
13 KRIBB_YJKIM ss84185422 Dec 14, 2007 (130)
14 HGSV ss84420198 Dec 14, 2007 (130)
15 BGI ss103279419 Dec 01, 2009 (131)
16 ILLUMINA ss122224658 Dec 01, 2009 (131)
17 ILLUMINA ss154269614 Dec 01, 2009 (131)
18 GMI ss157100026 Dec 01, 2009 (131)
19 ILLUMINA ss159446384 Dec 01, 2009 (131)
20 ILLUMINA ss160642276 Dec 01, 2009 (131)
21 COMPLETE_GENOMICS ss167848949 Jul 04, 2010 (132)
22 ILLUMINA ss171658598 Jul 04, 2010 (132)
23 AFFY ss173378104 Jul 04, 2010 (132)
24 ILLUMINA ss173640432 Jul 04, 2010 (132)
25 1000GENOMES ss211684880 Jul 14, 2010 (132)
26 1000GENOMES ss227146513 Jul 14, 2010 (132)
27 1000GENOMES ss236955850 Jul 15, 2010 (132)
28 1000GENOMES ss243309281 Jul 15, 2010 (132)
29 GMI ss282439287 May 04, 2012 (137)
30 ILLUMINA ss480835171 May 04, 2012 (137)
31 ILLUMINA ss480851481 May 04, 2012 (137)
32 ILLUMINA ss481783809 Sep 08, 2015 (146)
33 ILLUMINA ss485212411 May 04, 2012 (137)
34 ILLUMINA ss537194744 Sep 08, 2015 (146)
35 TISHKOFF ss564785685 Apr 25, 2013 (138)
36 SSMP ss660530360 Apr 25, 2013 (138)
37 ILLUMINA ss778524245 Sep 08, 2015 (146)
38 ILLUMINA ss783052172 Aug 21, 2014 (142)
39 ILLUMINA ss784010668 Sep 08, 2015 (146)
40 ILLUMINA ss825498060 Apr 01, 2015 (144)
41 ILLUMINA ss832310038 Apr 01, 2015 (144)
42 ILLUMINA ss832957946 Aug 21, 2014 (142)
43 ILLUMINA ss833548775 Aug 21, 2014 (142)
44 ILLUMINA ss833980694 Sep 08, 2015 (146)
45 EVA-GONL ss992288554 Aug 21, 2014 (142)
46 JMKIDD_LAB ss1080491336 Aug 21, 2014 (142)
47 1000GENOMES ss1355406117 Aug 21, 2014 (142)
48 DDI ss1427781288 Apr 01, 2015 (144)
49 EVA_GENOME_DK ss1577838499 Apr 01, 2015 (144)
50 EVA_UK10K_ALSPAC ss1634022238 Apr 01, 2015 (144)
51 EVA_UK10K_TWINSUK ss1677016271 Apr 01, 2015 (144)
52 EVA_DECODE ss1696324369 Apr 01, 2015 (144)
53 EVA_MGP ss1711418761 Apr 01, 2015 (144)
54 EVA_SVP ss1713526371 Apr 01, 2015 (144)
55 ILLUMINA ss1752181269 Sep 08, 2015 (146)
56 HAMMER_LAB ss1808425559 Sep 08, 2015 (146)
57 WEILL_CORNELL_DGM ss1935704033 Feb 12, 2016 (147)
58 ILLUMINA ss1946409106 Feb 12, 2016 (147)
59 ILLUMINA ss1959659629 Feb 12, 2016 (147)
60 JJLAB ss2028638721 Sep 14, 2016 (149)
61 USC_VALOUEV ss2157049924 Dec 20, 2016 (150)
62 HUMAN_LONGEVITY ss2210667993 Dec 20, 2016 (150)
63 TOPMED ss2375312744 Dec 20, 2016 (150)
64 TOPMED ss2375312745 Dec 20, 2016 (150)
65 SYSTEMSBIOZJU ss2628813643 Nov 08, 2017 (151)
66 ILLUMINA ss2633295546 Nov 08, 2017 (151)
67 GRF ss2701545470 Nov 08, 2017 (151)
68 ILLUMINA ss2710828154 Nov 08, 2017 (151)
69 GNOMAD ss2940367763 Nov 08, 2017 (151)
70 SWEGEN ss3014074476 Nov 08, 2017 (151)
71 ILLUMINA ss3021684649 Nov 08, 2017 (151)
72 BIOINF_KMB_FNS_UNIBA ss3028145158 Nov 08, 2017 (151)
73 TOPMED ss3240192756 Nov 08, 2017 (151)
74 TOPMED ss3240192757 Nov 08, 2017 (151)
75 CSHL ss3351340492 Nov 08, 2017 (151)
76 ILLUMINA ss3625687416 Oct 12, 2018 (152)
77 ILLUMINA ss3627479785 Oct 12, 2018 (152)
78 ILLUMINA ss3631283713 Oct 12, 2018 (152)
79 ILLUMINA ss3633114417 Oct 12, 2018 (152)
80 ILLUMINA ss3633820101 Oct 12, 2018 (152)
81 ILLUMINA ss3634632582 Oct 12, 2018 (152)
82 ILLUMINA ss3635508574 Oct 12, 2018 (152)
83 ILLUMINA ss3636322342 Oct 12, 2018 (152)
84 ILLUMINA ss3637259971 Oct 12, 2018 (152)
85 ILLUMINA ss3638113891 Oct 12, 2018 (152)
86 ILLUMINA ss3639069403 Oct 12, 2018 (152)
87 ILLUMINA ss3639540568 Oct 12, 2018 (152)
88 ILLUMINA ss3640339902 Oct 12, 2018 (152)
89 ILLUMINA ss3641068326 Oct 12, 2018 (152)
90 ILLUMINA ss3641363798 Oct 12, 2018 (152)
91 ILLUMINA ss3643095830 Oct 12, 2018 (152)
92 ILLUMINA ss3644662181 Oct 12, 2018 (152)
93 OMUKHERJEE_ADBS ss3646486176 Oct 12, 2018 (152)
94 ILLUMINA ss3652089304 Oct 12, 2018 (152)
95 EGCUT_WGS ss3681197502 Jul 13, 2019 (153)
96 EVA_DECODE ss3698850778 Jul 13, 2019 (153)
97 ILLUMINA ss3725544525 Jul 13, 2019 (153)
98 ACPOP ss3741341297 Jul 13, 2019 (153)
99 ILLUMINA ss3744138358 Jul 13, 2019 (153)
100 ILLUMINA ss3744933042 Jul 13, 2019 (153)
101 EVA ss3753693604 Jul 13, 2019 (153)
102 PAGE_CC ss3771866333 Jul 13, 2019 (153)
103 ILLUMINA ss3772431413 Jul 13, 2019 (153)
104 KHV_HUMAN_GENOMES ss3818990110 Jul 13, 2019 (153)
105 1000Genomes NC_000016.9 - 10624549 Oct 12, 2018 (152)
106 The Avon Longitudinal Study of Parents and Children NC_000016.9 - 10624549 Oct 12, 2018 (152)
107 Genetic variation in the Estonian population NC_000016.9 - 10624549 Oct 12, 2018 (152)
108 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 187010948 (NC_000016.9:10624548:C:C 31340/31346, NC_000016.9:10624548:C:G 6/31346)
Row 187010949 (NC_000016.9:10624548:C:C 27802/31346, NC_000016.9:10624548:C:T 3544/31346)

- Jul 13, 2019 (153)
109 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 187010948 (NC_000016.9:10624548:C:C 31340/31346, NC_000016.9:10624548:C:G 6/31346)
Row 187010949 (NC_000016.9:10624548:C:C 27802/31346, NC_000016.9:10624548:C:T 3544/31346)

- Jul 13, 2019 (153)
110 Northern Sweden NC_000016.9 - 10624549 Jul 13, 2019 (153)
111 The PAGE Study NC_000016.10 - 10530692 Jul 13, 2019 (153)
112 TopMed NC_000016.10 - 10530692 Oct 12, 2018 (152)
113 UK 10K study - Twins NC_000016.9 - 10624549 Oct 12, 2018 (152)
114 A Vietnamese Genetic Variation Database NC_000016.9 - 10624549 Jul 13, 2019 (153)
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)
rs57101817 May 23, 2008 (130)
rs117160297 Aug 16, 2010 (132)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss2375312744, ss2940367763 NC_000016.9:10624548:C:G NC_000016.10:10530691:C:G (self)
ss2210667993, ss3240192756 NC_000016.10:10530691:C:G NC_000016.10:10530691:C:G (self)
ss66213101, ss76359580, ss84420198, ss167848949, ss173378104, ss211684880, ss282439287, ss480835171, ss825498060, ss1696324369, ss1713526371, ss3639069403, ss3639540568, ss3643095830 NC_000016.8:10532049:C:T NC_000016.10:10530691:C:T (self)
68541784, 38057519, 26935750, 14626162, 38057519, 8457244, ss227146513, ss236955850, ss243309281, ss480851481, ss481783809, ss485212411, ss537194744, ss564785685, ss660530360, ss778524245, ss783052172, ss784010668, ss832310038, ss832957946, ss833548775, ss833980694, ss992288554, ss1080491336, ss1355406117, ss1427781288, ss1577838499, ss1634022238, ss1677016271, ss1711418761, ss1752181269, ss1808425559, ss1935704033, ss1946409106, ss1959659629, ss2028638721, ss2157049924, ss2375312745, ss2628813643, ss2633295546, ss2701545470, ss2710828154, ss2940367763, ss3014074476, ss3021684649, ss3351340492, ss3625687416, ss3627479785, ss3631283713, ss3633114417, ss3633820101, ss3634632582, ss3635508574, ss3636322342, ss3637259971, ss3638113891, ss3640339902, ss3641068326, ss3641363798, ss3644662181, ss3646486176, ss3652089304, ss3681197502, ss3741341297, ss3744138358, ss3744933042, ss3753693604, ss3772431413 NC_000016.9:10624548:C:T NC_000016.10:10530691:C:T (self)
1087802, 139712871, ss2210667993, ss3028145158, ss3240192757, ss3698850778, ss3725544525, ss3771866333, ss3818990110 NC_000016.10:10530691:C:T NC_000016.10:10530691:C:T (self)
ss10804094 NT_010393.13:1936760:C:T NC_000016.10:10530691:C:T (self)
ss4976496, ss66681750, ss67303443, ss67708420, ss69339050, ss70782094, ss71358608, ss75606524, ss79167542, ss84185422, ss103279419, ss122224658, ss154269614, ss157100026, ss159446384, ss160642276, ss171658598, ss173640432 NT_010393.16:10564548:C:T NC_000016.10:10530691:C:T (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 rs3790126

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.post308+0fe9b3b