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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.

rs3766951

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:28843047 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.356746 (94427/264690, TOPMED)
C=0.344068 (48824/141902, ALFA)
C=0.350831 (48983/139620, GnomAD) (+ 18 more)
C=0.18296 (5170/28258, 14KJPN)
C=0.18282 (3064/16760, 8.3KJPN)
C=0.3307 (2118/6404, 1000G_30x)
C=0.3211 (1608/5008, 1000G)
C=0.3299 (1478/4480, Estonian)
C=0.3256 (1255/3854, ALSPAC)
C=0.3304 (1225/3708, TWINSUK)
C=0.1937 (566/2922, KOREAN)
C=0.309 (308/998, GoNL)
C=0.176 (134/762, PRJEB37584)
C=0.348 (209/600, NorthernSweden)
C=0.320 (105/328, HapMap)
T=0.409 (131/320, SGDP_PRJ)
C=0.380 (82/216, Qatari)
C=0.189 (39/206, Vietnamese)
C=0.30 (12/40, GENOME_DK)
C=0.24 (8/34, Ancient Sardinia)
T=0.43 (12/28, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
OPRD1 : Intron Variant
Publications
7 citations
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 141902 T=0.655932 C=0.344068
European Sub 122778 T=0.659459 C=0.340541
African Sub 5510 T=0.6064 C=0.3936
African Others Sub 208 T=0.659 C=0.341
African American Sub 5302 T=0.6043 C=0.3957
Asian Sub 618 T=0.788 C=0.212
East Asian Sub 488 T=0.801 C=0.199
Other Asian Sub 130 T=0.738 C=0.262
Latin American 1 Sub 730 T=0.668 C=0.332
Latin American 2 Sub 6262 T=0.6041 C=0.3959
South Asian Sub 184 T=0.701 C=0.299
Other Sub 5820 T=0.6672 C=0.3328


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 T=0.643254 C=0.356746
Allele Frequency Aggregator Total Global 141902 T=0.655932 C=0.344068
Allele Frequency Aggregator European Sub 122778 T=0.659459 C=0.340541
Allele Frequency Aggregator Latin American 2 Sub 6262 T=0.6041 C=0.3959
Allele Frequency Aggregator Other Sub 5820 T=0.6672 C=0.3328
Allele Frequency Aggregator African Sub 5510 T=0.6064 C=0.3936
Allele Frequency Aggregator Latin American 1 Sub 730 T=0.668 C=0.332
Allele Frequency Aggregator Asian Sub 618 T=0.788 C=0.212
Allele Frequency Aggregator South Asian Sub 184 T=0.701 C=0.299
gnomAD - Genomes Global Study-wide 139620 T=0.649169 C=0.350831
gnomAD - Genomes European Sub 75644 T=0.67207 C=0.32793
gnomAD - Genomes African Sub 41810 T=0.60110 C=0.39890
gnomAD - Genomes American Sub 13580 T=0.63741 C=0.36259
gnomAD - Genomes Ashkenazi Jewish Sub 3320 T=0.6413 C=0.3587
gnomAD - Genomes East Asian Sub 3126 T=0.8081 C=0.1919
gnomAD - Genomes Other Sub 2140 T=0.6336 C=0.3664
14KJPN JAPANESE Study-wide 28258 T=0.81704 C=0.18296
8.3KJPN JAPANESE Study-wide 16760 T=0.81718 C=0.18282
1000Genomes_30x Global Study-wide 6404 T=0.6693 C=0.3307
1000Genomes_30x African Sub 1786 T=0.5789 C=0.4211
1000Genomes_30x Europe Sub 1266 T=0.6422 C=0.3578
1000Genomes_30x South Asian Sub 1202 T=0.7429 C=0.2571
1000Genomes_30x East Asian Sub 1170 T=0.8111 C=0.1889
1000Genomes_30x American Sub 980 T=0.609 C=0.391
1000Genomes Global Study-wide 5008 T=0.6789 C=0.3211
1000Genomes African Sub 1322 T=0.5855 C=0.4145
1000Genomes East Asian Sub 1008 T=0.8145 C=0.1855
1000Genomes Europe Sub 1006 T=0.6412 C=0.3588
1000Genomes South Asian Sub 978 T=0.753 C=0.247
1000Genomes American Sub 694 T=0.611 C=0.389
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.6701 C=0.3299
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.6744 C=0.3256
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.6696 C=0.3304
KOREAN population from KRGDB KOREAN Study-wide 2922 T=0.8063 C=0.1937
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.691 C=0.309
CNV burdens in cranial meningiomas Global Study-wide 762 T=0.824 C=0.176
CNV burdens in cranial meningiomas CRM Sub 762 T=0.824 C=0.176
Northern Sweden ACPOP Study-wide 600 T=0.652 C=0.348
HapMap Global Study-wide 328 T=0.680 C=0.320
HapMap African Sub 120 T=0.575 C=0.425
HapMap American Sub 120 T=0.717 C=0.283
HapMap Asian Sub 88 T=0.77 C=0.23
SGDP_PRJ Global Study-wide 320 T=0.409 C=0.591
Qatari Global Study-wide 216 T=0.620 C=0.380
A Vietnamese Genetic Variation Database Global Study-wide 206 T=0.811 C=0.189
The Danish reference pan genome Danish Study-wide 40 T=0.70 C=0.30
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 34 T=0.76 C=0.24
Siberian Global Study-wide 28 T=0.43 C=0.57
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.p14 chr 1 NC_000001.11:g.28843047T>C
GRCh37.p13 chr 1 NC_000001.10:g.29169559T>C
Gene: OPRD1, opioid receptor delta 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
OPRD1 transcript NM_000911.4:c.228-15907T>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

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= C
GRCh38.p14 chr 1 NC_000001.11:g.28843047= NC_000001.11:g.28843047T>C
GRCh37.p13 chr 1 NC_000001.10:g.29169559= NC_000001.10:g.29169559T>C
OPRD1 transcript NM_000911.3:c.228-15907= NM_000911.3:c.228-15907T>C
OPRD1 transcript NM_000911.4:c.228-15907= NM_000911.4:c.228-15907T>C
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#.

90 SubSNP, 21 Frequency submissions
No Submitter Submission ID Date (Build)
1 YUSUKE ss4952994 Aug 28, 2002 (107)
2 PERLEGEN ss16333724 Feb 28, 2004 (123)
3 PERLEGEN ss23148231 Sep 20, 2004 (123)
4 ABI ss44016878 Mar 14, 2006 (126)
5 AFFY ss65979231 Nov 29, 2006 (127)
6 PERLEGEN ss68762118 May 16, 2007 (127)
7 1000GENOMES ss108083847 Jan 22, 2009 (130)
8 1000GENOMES ss110223941 Jan 24, 2009 (130)
9 GMI ss154806348 Dec 01, 2009 (131)
10 ILLUMINA ss160638981 Dec 01, 2009 (131)
11 ENSEMBL ss161243949 Dec 01, 2009 (131)
12 COMPLETE_GENOMICS ss163215980 Jul 04, 2010 (132)
13 COMPLETE_GENOMICS ss166287517 Jul 04, 2010 (132)
14 1000GENOMES ss218298994 Jul 14, 2010 (132)
15 1000GENOMES ss230473313 Jul 14, 2010 (132)
16 1000GENOMES ss238178029 Jul 15, 2010 (132)
17 GMI ss275764566 May 04, 2012 (137)
18 GMI ss284024619 Apr 25, 2013 (138)
19 PJP ss290796160 May 09, 2011 (134)
20 ILLUMINA ss480824162 May 04, 2012 (137)
21 ILLUMINA ss480839913 May 04, 2012 (137)
22 ILLUMINA ss481770655 Sep 08, 2015 (146)
23 ILLUMINA ss485206877 May 04, 2012 (137)
24 ILLUMINA ss537191327 Sep 08, 2015 (146)
25 TISHKOFF ss553927746 Apr 25, 2013 (138)
26 SSMP ss647662263 Apr 25, 2013 (138)
27 ILLUMINA ss778895409 Sep 08, 2015 (146)
28 ILLUMINA ss783049423 Sep 08, 2015 (146)
29 ILLUMINA ss784008023 Sep 08, 2015 (146)
30 ILLUMINA ss832307253 Sep 08, 2015 (146)
31 ILLUMINA ss834356595 Sep 08, 2015 (146)
32 EVA-GONL ss974982219 Aug 21, 2014 (142)
33 JMKIDD_LAB ss1067758091 Aug 21, 2014 (142)
34 1000GENOMES ss1290182104 Aug 21, 2014 (142)
35 DDI ss1425756539 Apr 01, 2015 (144)
36 EVA_GENOME_DK ss1573960104 Apr 01, 2015 (144)
37 EVA_DECODE ss1584341885 Apr 01, 2015 (144)
38 EVA_UK10K_ALSPAC ss1599801448 Apr 01, 2015 (144)
39 EVA_UK10K_TWINSUK ss1642795481 Apr 01, 2015 (144)
40 ILLUMINA ss1751914254 Sep 08, 2015 (146)
41 HAMMER_LAB ss1794109047 Sep 08, 2015 (146)
42 WEILL_CORNELL_DGM ss1918193864 Feb 12, 2016 (147)
43 GENOMED ss1966710820 Jul 19, 2016 (147)
44 JJLAB ss2019608170 Sep 14, 2016 (149)
45 USC_VALOUEV ss2147616072 Dec 20, 2016 (150)
46 HUMAN_LONGEVITY ss2161028881 Dec 20, 2016 (150)
47 SYSTEMSBIOZJU ss2624320320 Nov 08, 2017 (151)
48 ILLUMINA ss2632494127 Nov 08, 2017 (151)
49 GRF ss2697521550 Nov 08, 2017 (151)
50 GNOMAD ss2753109263 Nov 08, 2017 (151)
51 SWEGEN ss2986528278 Nov 08, 2017 (151)
52 BIOINF_KMB_FNS_UNIBA ss3023569142 Nov 08, 2017 (151)
53 CSHL ss3343381562 Nov 08, 2017 (151)
54 ILLUMINA ss3626056863 Oct 11, 2018 (152)
55 ILLUMINA ss3630531408 Oct 11, 2018 (152)
56 ILLUMINA ss3632885432 Oct 11, 2018 (152)
57 ILLUMINA ss3633579617 Oct 11, 2018 (152)
58 ILLUMINA ss3634314820 Oct 11, 2018 (152)
59 ILLUMINA ss3635273623 Oct 11, 2018 (152)
60 ILLUMINA ss3635990701 Oct 11, 2018 (152)
61 ILLUMINA ss3637024010 Oct 11, 2018 (152)
62 ILLUMINA ss3640022183 Oct 11, 2018 (152)
63 EGCUT_WGS ss3654591380 Jul 12, 2019 (153)
64 EVA_DECODE ss3686420943 Jul 12, 2019 (153)
65 ACPOP ss3726898450 Jul 12, 2019 (153)
66 ILLUMINA ss3744615770 Jul 12, 2019 (153)
67 EVA ss3745983029 Jul 12, 2019 (153)
68 ILLUMINA ss3772117310 Jul 12, 2019 (153)
69 KHV_HUMAN_GENOMES ss3799002414 Jul 12, 2019 (153)
70 EVA ss3826088448 Apr 25, 2020 (154)
71 SGDP_PRJ ss3848485445 Apr 25, 2020 (154)
72 KRGDB ss3893421172 Apr 25, 2020 (154)
73 EVA ss3984454354 Apr 27, 2021 (155)
74 EVA ss3984785884 Apr 27, 2021 (155)
75 EVA ss4016900317 Apr 27, 2021 (155)
76 TOPMED ss4443446018 Apr 27, 2021 (155)
77 TOMMO_GENOMICS ss5143114957 Apr 27, 2021 (155)
78 1000G_HIGH_COVERAGE ss5241644390 Oct 13, 2022 (156)
79 EVA ss5314602929 Oct 13, 2022 (156)
80 EVA ss5317579404 Oct 13, 2022 (156)
81 HUGCELL_USP ss5442777536 Oct 13, 2022 (156)
82 1000G_HIGH_COVERAGE ss5513615061 Oct 13, 2022 (156)
83 SANFORD_IMAGENETICS ss5625183635 Oct 13, 2022 (156)
84 TOMMO_GENOMICS ss5667618983 Oct 13, 2022 (156)
85 EVA ss5799478973 Oct 13, 2022 (156)
86 YY_MCH ss5800442544 Oct 13, 2022 (156)
87 EVA ss5831720321 Oct 13, 2022 (156)
88 EVA ss5848835667 Oct 13, 2022 (156)
89 EVA ss5907543847 Oct 13, 2022 (156)
90 EVA ss5936999740 Oct 13, 2022 (156)
91 1000Genomes NC_000001.10 - 29169559 Oct 11, 2018 (152)
92 1000Genomes_30x NC_000001.11 - 28843047 Oct 13, 2022 (156)
93 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 29169559 Oct 11, 2018 (152)
94 Genetic variation in the Estonian population NC_000001.10 - 29169559 Oct 11, 2018 (152)
95 The Danish reference pan genome NC_000001.10 - 29169559 Apr 25, 2020 (154)
96 gnomAD - Genomes NC_000001.11 - 28843047 Apr 27, 2021 (155)
97 Genome of the Netherlands Release 5 NC_000001.10 - 29169559 Apr 25, 2020 (154)
98 HapMap NC_000001.11 - 28843047 Apr 25, 2020 (154)
99 KOREAN population from KRGDB NC_000001.10 - 29169559 Apr 25, 2020 (154)
100 Northern Sweden NC_000001.10 - 29169559 Jul 12, 2019 (153)
101 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 29169559 Apr 27, 2021 (155)
102 CNV burdens in cranial meningiomas NC_000001.10 - 29169559 Apr 27, 2021 (155)
103 Qatari NC_000001.10 - 29169559 Apr 25, 2020 (154)
104 SGDP_PRJ NC_000001.10 - 29169559 Apr 25, 2020 (154)
105 Siberian NC_000001.10 - 29169559 Apr 25, 2020 (154)
106 8.3KJPN NC_000001.10 - 29169559 Apr 27, 2021 (155)
107 14KJPN NC_000001.11 - 28843047 Oct 13, 2022 (156)
108 TopMed NC_000001.11 - 28843047 Apr 27, 2021 (155)
109 UK 10K study - Twins NC_000001.10 - 29169559 Oct 11, 2018 (152)
110 A Vietnamese Genetic Variation Database NC_000001.10 - 29169559 Jul 12, 2019 (153)
111 ALFA NC_000001.11 - 28843047 Apr 27, 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)
rs11564797 Sep 24, 2004 (123)
rs16837722 Oct 07, 2004 (123)
rs386585862 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss108083847, ss110223941, ss163215980, ss166287517, ss275764566, ss284024619, ss290796160, ss480824162, ss1584341885 NC_000001.9:29042145:T:C NC_000001.11:28843046:T:C (self)
875542, 466674, 329628, 1438046, 200140, 598566, 183315, 11811, 3657, 235794, 502425, 132426, 1084264, 466674, 95894, ss218298994, ss230473313, ss238178029, ss480839913, ss481770655, ss485206877, ss537191327, ss553927746, ss647662263, ss778895409, ss783049423, ss784008023, ss832307253, ss834356595, ss974982219, ss1067758091, ss1290182104, ss1425756539, ss1573960104, ss1599801448, ss1642795481, ss1751914254, ss1794109047, ss1918193864, ss1966710820, ss2019608170, ss2147616072, ss2624320320, ss2632494127, ss2697521550, ss2753109263, ss2986528278, ss3343381562, ss3626056863, ss3630531408, ss3632885432, ss3633579617, ss3634314820, ss3635273623, ss3635990701, ss3637024010, ss3640022183, ss3654591380, ss3726898450, ss3744615770, ss3745983029, ss3772117310, ss3826088448, ss3848485445, ss3893421172, ss3984454354, ss3984785884, ss4016900317, ss5143114957, ss5314602929, ss5317579404, ss5625183635, ss5799478973, ss5831720321, ss5936999740 NC_000001.10:29169558:T:C NC_000001.11:28843046:T:C (self)
1140996, 6177171, 35700, 1456087, 7052353, 13256192795, ss2161028881, ss3023569142, ss3686420943, ss3799002414, ss4443446018, ss5241644390, ss5442777536, ss5513615061, ss5667618983, ss5800442544, ss5848835667, ss5907543847 NC_000001.11:28843046:T:C NC_000001.11:28843046:T:C (self)
ss4952994, ss16333724, ss23148231, ss44016878, ss65979231, ss68762118, ss154806348, ss160638981, ss161243949 NT_004610.19:15849646:T:C NC_000001.11:28843046: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.

7 citations for rs3766951
PMID Title Author Year Journal
18518925 Genetic susceptibility to heroin addiction: a candidate gene association study. Levran O et al. 2008 Genes, brain, and behavior
19500151 Heroin addiction in African Americans: a hypothesis-driven association study. Levran O et al. 2009 Genes, brain, and behavior
22020140 Molecular mechanisms of opioid receptor-dependent signaling and behavior. Al-Hasani R et al. 2011 Anesthesiology
22500942 Association of OPRD1 polymorphisms with heroin dependence in a large case-control series. Nelson EC et al. 2014 Addiction biology
22547174 The genetics of the opioid system and specific drug addictions. Levran O et al. 2012 Human genetics
28035534 OPRD1 Genetic Variation and Human Disease. Crist RC et al. 2018 Handbook of experimental pharmacology
28976288 The μ-opioid receptor nonsynonymous variant 118A>G is associated with prolonged abstinence from heroin without agonist treatment. Levran O et al. 2017 Pharmacogenomics
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.post761+d5e8e07