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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.

rs737864

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr22:19942636 (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
C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.227583 (60239/264690, TOPMED)
T=0.229076 (32083/140054, GnomAD)
T=0.25376 (9994/39384, ALFA) (+ 15 more)
T=0.24720 (4143/16760, 8.3KJPN)
T=0.2266 (1135/5008, 1000G)
T=0.2353 (1054/4480, Estonian)
T=0.2841 (1095/3854, ALSPAC)
T=0.2915 (1081/3708, TWINSUK)
T=0.2898 (849/2930, KOREAN)
T=0.2893 (530/1832, Korea1K)
T=0.277 (276/998, GoNL)
T=0.240 (144/600, NorthernSweden)
T=0.258 (62/240, PharmGKB)
T=0.264 (57/216, Qatari)
T=0.361 (78/216, Vietnamese)
C=0.406 (86/212, SGDP_PRJ)
T=0.23 (9/40, GENOME_DK)
C=0.31 (8/26, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
COMT : Intron Variant
TXNRD2 : 2KB Upstream Variant
Publications
3 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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 39384 C=0.74624 G=0.00000, T=0.25376
European Sub 30472 C=0.72608 G=0.00000, T=0.27392
African Sub 5652 C=0.8592 G=0.0000, T=0.1408
African Others Sub 194 C=0.892 G=0.000, T=0.108
African American Sub 5458 C=0.8580 G=0.0000, T=0.1420
Asian Sub 128 C=0.742 G=0.000, T=0.258
East Asian Sub 100 C=0.74 G=0.00, T=0.26
Other Asian Sub 28 C=0.75 G=0.00, T=0.25
Latin American 1 Sub 168 C=0.702 G=0.000, T=0.298
Latin American 2 Sub 700 C=0.854 G=0.000, T=0.146
South Asian Sub 114 C=0.754 G=0.000, T=0.246
Other Sub 2150 C=0.7033 G=0.0000, T=0.2967


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").

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Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 C=0.772417 T=0.227583
gnomAD - Genomes Global Study-wide 140054 C=0.770924 T=0.229076
gnomAD - Genomes European Sub 75858 C=0.73681 T=0.26319
gnomAD - Genomes African Sub 41950 C=0.85006 T=0.14994
gnomAD - Genomes American Sub 13646 C=0.77891 T=0.22109
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=0.5692 T=0.4308
gnomAD - Genomes East Asian Sub 3128 C=0.7318 T=0.2682
gnomAD - Genomes Other Sub 2150 C=0.7484 T=0.2516
Allele Frequency Aggregator Total Global 39384 C=0.74624 G=0.00000, T=0.25376
Allele Frequency Aggregator European Sub 30472 C=0.72608 G=0.00000, T=0.27392
Allele Frequency Aggregator African Sub 5652 C=0.8592 G=0.0000, T=0.1408
Allele Frequency Aggregator Other Sub 2150 C=0.7033 G=0.0000, T=0.2967
Allele Frequency Aggregator Latin American 2 Sub 700 C=0.854 G=0.000, T=0.146
Allele Frequency Aggregator Latin American 1 Sub 168 C=0.702 G=0.000, T=0.298
Allele Frequency Aggregator Asian Sub 128 C=0.742 G=0.000, T=0.258
Allele Frequency Aggregator South Asian Sub 114 C=0.754 G=0.000, T=0.246
8.3KJPN JAPANESE Study-wide 16760 C=0.75280 T=0.24720
1000Genomes Global Study-wide 5008 C=0.7734 T=0.2266
1000Genomes African Sub 1322 C=0.8737 T=0.1263
1000Genomes East Asian Sub 1008 C=0.7063 T=0.2937
1000Genomes Europe Sub 1006 C=0.7187 T=0.2813
1000Genomes South Asian Sub 978 C=0.733 T=0.267
1000Genomes American Sub 694 C=0.816 T=0.184
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.7647 T=0.2353
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.7159 T=0.2841
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.7085 T=0.2915
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.7102 T=0.2898
Korean Genome Project KOREAN Study-wide 1832 C=0.7107 T=0.2893
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.723 T=0.277
Northern Sweden ACPOP Study-wide 600 C=0.760 T=0.240
PharmGKB Aggregated Global Study-wide 240 C=0.742 T=0.258
PharmGKB Aggregated PA151927220 Sub 240 C=0.742 T=0.258
Qatari Global Study-wide 216 C=0.736 T=0.264
A Vietnamese Genetic Variation Database Global Study-wide 216 C=0.639 T=0.361
SGDP_PRJ Global Study-wide 212 C=0.406 T=0.594
The Danish reference pan genome Danish Study-wide 40 C=0.78 T=0.23
Siberian Global Study-wide 26 C=0.31 T=0.69
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 22 NC_000022.11:g.19942636C>G
GRCh38.p13 chr 22 NC_000022.11:g.19942636C>T
GRCh37.p13 chr 22 NC_000022.10:g.19930159C>G
GRCh37.p13 chr 22 NC_000022.10:g.19930159C>T
TXNRD2 RefSeqGene (LRG_417) NG_011835.1:g.4201G>C
TXNRD2 RefSeqGene (LRG_417) NG_011835.1:g.4201G>A
COMT RefSeqGene (LRG_1010) NG_011526.1:g.5897C>G
COMT RefSeqGene (LRG_1010) NG_011526.1:g.5897C>T
Gene: COMT, catechol-O-methyltransferase (plus strand)
Molecule type Change Amino acid[Codon] SO Term
COMT transcript variant 1 NM_000754.4:c.-92+739C>G N/A Intron Variant
COMT transcript variant 5 NM_001362828.2:c.-386+739…

NM_001362828.2:c.-386+739C>G

N/A Intron Variant
COMT transcript variant 2 NM_001135161.2:c. N/A Genic Upstream Transcript Variant
COMT transcript variant 3 NM_001135162.2:c. N/A Genic Upstream Transcript Variant
COMT transcript variant 4 NM_007310.3:c. N/A Genic Upstream Transcript Variant
Gene: TXNRD2, thioredoxin reductase 2 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
TXNRD2 transcript variant 5 NM_001282512.3:c. N/A Upstream Transcript Variant
TXNRD2 transcript variant 2 NM_001352300.2:c. N/A Upstream Transcript Variant
TXNRD2 transcript variant 1 NM_006440.5:c. N/A Upstream Transcript Variant
TXNRD2 transcript variant 3 NM_001352301.2:c. N/A N/A
TXNRD2 transcript variant 4 NM_001352302.2:c. N/A N/A
TXNRD2 transcript variant 6 NM_001352303.2:c. N/A N/A
TXNRD2 transcript variant 7 NR_147957.2:n. N/A 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
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
GRCh38.p13 chr 22 NC_000022.11:g.19942636= NC_000022.11:g.19942636C>G NC_000022.11:g.19942636C>T
GRCh37.p13 chr 22 NC_000022.10:g.19930159= NC_000022.10:g.19930159C>G NC_000022.10:g.19930159C>T
TXNRD2 RefSeqGene (LRG_417) NG_011835.1:g.4201= NG_011835.1:g.4201G>C NG_011835.1:g.4201G>A
COMT RefSeqGene (LRG_1010) NG_011526.1:g.5897= NG_011526.1:g.5897C>G NG_011526.1:g.5897C>T
COMT transcript variant 1 NM_000754.3:c.-92+739= NM_000754.3:c.-92+739C>G NM_000754.3:c.-92+739C>T
COMT transcript variant 1 NM_000754.4:c.-92+739= NM_000754.4:c.-92+739C>G NM_000754.4:c.-92+739C>T
COMT transcript variant 5 NM_001362828.2:c.-386+739= NM_001362828.2:c.-386+739C>G NM_001362828.2:c.-386+739C>T
COMT transcript variant X1 XM_005261229.1:c.-386+739= XM_005261229.1:c.-386+739C>G XM_005261229.1:c.-386+739C>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#.

66 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss84950 Oct 05, 2000 (86)
2 SC_JCM ss6288090 Feb 20, 2003 (111)
3 EGP_SNPS ss12673695 Dec 05, 2003 (119)
4 PERLEGEN ss24556294 Sep 20, 2004 (123)
5 ABI ss44310525 Mar 13, 2006 (126)
6 EGP_SNPS ss66862083 Dec 02, 2006 (127)
7 PHARMGKB_PPII ss84140185 Dec 14, 2007 (130)
8 BCMHGSC_JDW ss91877465 Mar 24, 2008 (129)
9 1000GENOMES ss112551327 Jan 25, 2009 (130)
10 GMI ss157034305 Dec 01, 2009 (131)
11 COMPLETE_GENOMICS ss167682542 Jul 04, 2010 (132)
12 1000GENOMES ss228618055 Jul 14, 2010 (132)
13 1000GENOMES ss238022240 Jul 15, 2010 (132)
14 1000GENOMES ss244151610 Jul 15, 2010 (132)
15 BL ss255842426 May 09, 2011 (134)
16 GMI ss283587128 May 04, 2012 (137)
17 GMI ss287550202 Apr 25, 2013 (138)
18 ILLUMINA ss479159445 May 04, 2012 (137)
19 ILLUMINA ss484289252 May 04, 2012 (137)
20 ILLUMINA ss532755552 Sep 08, 2015 (146)
21 TISHKOFF ss566560655 Apr 25, 2013 (138)
22 SSMP ss662483625 Apr 25, 2013 (138)
23 ILLUMINA ss779534657 Sep 08, 2015 (146)
24 ILLUMINA ss780911938 Sep 08, 2015 (146)
25 ILLUMINA ss835005268 Sep 08, 2015 (146)
26 EVA-GONL ss995222586 Aug 21, 2014 (142)
27 JMKIDD_LAB ss1082570341 Aug 21, 2014 (142)
28 1000GENOMES ss1366682430 Aug 21, 2014 (142)
29 DDI ss1429219717 Apr 01, 2015 (144)
30 EVA_GENOME_DK ss1579704198 Apr 01, 2015 (144)
31 EVA_UK10K_ALSPAC ss1639753624 Apr 01, 2015 (144)
32 EVA_UK10K_TWINSUK ss1682747657 Apr 01, 2015 (144)
33 EVA_DECODE ss1699291710 Apr 01, 2015 (144)
34 HAMMER_LAB ss1809733893 Sep 08, 2015 (146)
35 WEILL_CORNELL_DGM ss1938784175 Feb 12, 2016 (147)
36 JJLAB ss2030165112 Sep 14, 2016 (149)
37 USC_VALOUEV ss2158775026 Dec 20, 2016 (150)
38 HUMAN_LONGEVITY ss2246455620 Dec 20, 2016 (150)
39 TOPMED ss2413282476 Dec 20, 2016 (150)
40 SYSTEMSBIOZJU ss2629580685 Nov 08, 2017 (151)
41 ILLUMINA ss2633862725 Nov 08, 2017 (151)
42 GRF ss2704517966 Nov 08, 2017 (151)
43 GNOMAD ss2972984366 Nov 08, 2017 (151)
44 AFFY ss2985233263 Nov 08, 2017 (151)
45 AFFY ss2985850617 Nov 08, 2017 (151)
46 SWEGEN ss3019086016 Nov 08, 2017 (151)
47 BIOINF_KMB_FNS_UNIBA ss3028920256 Nov 08, 2017 (151)
48 CSHL ss3352776386 Nov 08, 2017 (151)
49 TOPMED ss3374056859 Nov 08, 2017 (151)
50 ILLUMINA ss3628505956 Oct 12, 2018 (152)
51 ILLUMINA ss3631815131 Oct 12, 2018 (152)
52 ILLUMINA ss3642211194 Oct 12, 2018 (152)
53 ILLUMINA ss3654001325 Oct 12, 2018 (152)
54 EGCUT_WGS ss3685618568 Jul 13, 2019 (153)
55 EVA_DECODE ss3707954570 Jul 13, 2019 (153)
56 ACPOP ss3743823085 Jul 13, 2019 (153)
57 EVA ss3759230686 Jul 13, 2019 (153)
58 KHV_HUMAN_GENOMES ss3822398589 Jul 13, 2019 (153)
59 EVA ss3835927687 Apr 27, 2020 (154)
60 EVA ss3841592348 Apr 27, 2020 (154)
61 EVA ss3847107005 Apr 27, 2020 (154)
62 SGDP_PRJ ss3890256410 Apr 27, 2020 (154)
63 KRGDB ss3940639890 Apr 27, 2020 (154)
64 KOGIC ss3983389236 Apr 27, 2020 (154)
65 TOPMED ss5105102556 Apr 26, 2021 (155)
66 TOMMO_GENOMICS ss5232039687 Apr 26, 2021 (155)
67 1000Genomes NC_000022.10 - 19930159 Oct 12, 2018 (152)
68 The Avon Longitudinal Study of Parents and Children NC_000022.10 - 19930159 Oct 12, 2018 (152)
69 Genetic variation in the Estonian population NC_000022.10 - 19930159 Oct 12, 2018 (152)
70 The Danish reference pan genome NC_000022.10 - 19930159 Apr 27, 2020 (154)
71 gnomAD - Genomes NC_000022.11 - 19942636 Apr 26, 2021 (155)
72 Genome of the Netherlands Release 5 NC_000022.10 - 19930159 Apr 27, 2020 (154)
73 KOREAN population from KRGDB NC_000022.10 - 19930159 Apr 27, 2020 (154)
74 Korean Genome Project NC_000022.11 - 19942636 Apr 27, 2020 (154)
75 Northern Sweden NC_000022.10 - 19930159 Jul 13, 2019 (153)
76 PharmGKB Aggregated NC_000022.11 - 19942636 Apr 27, 2020 (154)
77 Qatari NC_000022.10 - 19930159 Apr 27, 2020 (154)
78 SGDP_PRJ NC_000022.10 - 19930159 Apr 27, 2020 (154)
79 Siberian NC_000022.10 - 19930159 Apr 27, 2020 (154)
80 8.3KJPN NC_000022.10 - 19930159 Apr 26, 2021 (155)
81 TopMed NC_000022.11 - 19942636 Apr 26, 2021 (155)
82 UK 10K study - Twins NC_000022.10 - 19930159 Oct 12, 2018 (152)
83 A Vietnamese Genetic Variation Database NC_000022.10 - 19930159 Jul 13, 2019 (153)
84 ALFA NC_000022.11 - 19942636 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)
rs17534169 Oct 07, 2004 (123)
rs57151413 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
11053834484 NC_000022.11:19942635:C:G NC_000022.11:19942635:C:G
ss91877465, ss112551327, ss167682542, ss255842426, ss283587128, ss287550202, ss484289252, ss1699291710 NC_000022.9:18310158:C:T NC_000022.11:19942635:C:T (self)
80216840, 44381654, 31356816, 5869137, 19773708, 47817284, 17107950, 20826097, 42273390, 11291380, 90008994, 44381654, 9792445, ss228618055, ss238022240, ss244151610, ss479159445, ss532755552, ss566560655, ss662483625, ss779534657, ss780911938, ss835005268, ss995222586, ss1082570341, ss1366682430, ss1429219717, ss1579704198, ss1639753624, ss1682747657, ss1809733893, ss1938784175, ss2030165112, ss2158775026, ss2413282476, ss2629580685, ss2633862725, ss2704517966, ss2972984366, ss2985233263, ss2985850617, ss3019086016, ss3352776386, ss3628505956, ss3631815131, ss3642211194, ss3654001325, ss3685618568, ss3743823085, ss3759230686, ss3835927687, ss3841592348, ss3890256410, ss3940639890, ss5232039687 NC_000022.10:19930158:C:T NC_000022.11:19942635:C:T (self)
566538969, 39767237, 7552, 237439938, 380211503, 11053834484, ss2246455620, ss3028920256, ss3374056859, ss3707954570, ss3822398589, ss3847107005, ss3983389236, ss5105102556 NC_000022.11:19942635:C:T NC_000022.11:19942635:C:T (self)
ss84950, ss6288090, ss12673695, ss24556294, ss44310525, ss66862083, ss84140185, ss157034305 NT_011519.10:3082308:C:T NC_000022.11:19942635: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.

3 citations for rs737864
PMID Title Author Year Journal
16837108 Haplotypes in cathechol-O-methyltransferase gene confer increased risk for psychosis in Alzheimer disease. Borroni B et al. 2007 Neurobiology of aging
17622328 Analysis of TBX1 variation in patients with psychotic and affective disorders. Funke BH et al. 2007 Molecular medicine (Cambridge, Mass.)
20157235 Genetics of psychosis in Alzheimer's disease: a review. DeMichele-Sweet MA et al. 2010 Journal of Alzheimer's disease
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.post676+237644a