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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.

rs979606

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chrX:43741895 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.264559 (70026/264690, TOPMED)
C=0.284379 (35962/126458, ALFA)
T=0.41574 (9239/22223, 14KJPN) (+ 13 more)
T=0.41493 (5329/12843, 8.3KJPN)
C=0.3625 (1742/4805, 1000G_30x)
C=0.3743 (1413/3775, 1000G)
C=0.2910 (1079/3708, TWINSUK)
T=0.4471 (1310/2930, KOREAN)
C=0.3008 (869/2889, ALSPAC)
C=0.3307 (625/1890, HapMap)
C=0.264 (141/534, MGP)
C=0.115 (44/384, SGDP_PRJ)
C=0.194 (21/108, Qatari)
T=0.44 (21/48, Vietnamese)
C=0.20 (8/40, GENOME_DK)
C=0.22 (8/36, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MAOA : Intron Variant
Publications
10 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 126458 C=0.284379 T=0.715621
European Sub 106550 C=0.293552 T=0.706448
African Sub 9937 C=0.1487 T=0.8513
African Others Sub 338 C=0.121 T=0.879
African American Sub 9599 C=0.1497 T=0.8503
Asian Sub 678 C=0.588 T=0.412
East Asian Sub 514 C=0.595 T=0.405
Other Asian Sub 164 C=0.567 T=0.433
Latin American 1 Sub 756 C=0.251 T=0.749
Latin American 2 Sub 2402 C=0.3056 T=0.6944
South Asian Sub 196 C=0.663 T=0.337
Other Sub 5939 C=0.2952 T=0.7048


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 C=0.264559 T=0.735441
Allele Frequency Aggregator Total Global 126458 C=0.284379 T=0.715621
Allele Frequency Aggregator European Sub 106550 C=0.293552 T=0.706448
Allele Frequency Aggregator African Sub 9937 C=0.1487 T=0.8513
Allele Frequency Aggregator Other Sub 5939 C=0.2952 T=0.7048
Allele Frequency Aggregator Latin American 2 Sub 2402 C=0.3056 T=0.6944
Allele Frequency Aggregator Latin American 1 Sub 756 C=0.251 T=0.749
Allele Frequency Aggregator Asian Sub 678 C=0.588 T=0.412
Allele Frequency Aggregator South Asian Sub 196 C=0.663 T=0.337
14KJPN JAPANESE Study-wide 22223 C=0.58426 T=0.41574
8.3KJPN JAPANESE Study-wide 12843 C=0.58507 T=0.41493
1000Genomes_30x Global Study-wide 4805 C=0.3625 T=0.6375
1000Genomes_30x African Sub 1328 C=0.1393 T=0.8607
1000Genomes_30x Europe Sub 961 C=0.279 T=0.721
1000Genomes_30x South Asian Sub 883 C=0.648 T=0.352
1000Genomes_30x East Asian Sub 878 C=0.571 T=0.429
1000Genomes_30x American Sub 755 C=0.286 T=0.714
1000Genomes Global Study-wide 3775 C=0.3743 T=0.6257
1000Genomes African Sub 1003 C=0.1366 T=0.8634
1000Genomes Europe Sub 766 C=0.287 T=0.713
1000Genomes East Asian Sub 764 C=0.572 T=0.428
1000Genomes South Asian Sub 718 C=0.648 T=0.352
1000Genomes American Sub 524 C=0.294 T=0.706
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.2910 T=0.7090
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.5529 T=0.4471
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 2889 C=0.3008 T=0.6992
HapMap Global Study-wide 1890 C=0.3307 T=0.6693
HapMap American Sub 770 C=0.429 T=0.571
HapMap African Sub 690 C=0.138 T=0.862
HapMap Asian Sub 254 C=0.575 T=0.425
HapMap Europe Sub 176 C=0.307 T=0.693
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 C=0.264 T=0.736
SGDP_PRJ Global Study-wide 384 C=0.115 T=0.885
Qatari Global Study-wide 108 C=0.194 T=0.806
A Vietnamese Genetic Variation Database Global Study-wide 48 C=0.56 T=0.44
The Danish reference pan genome Danish Study-wide 40 C=0.20 T=0.80
Siberian Global Study-wide 36 C=0.22 T=0.78
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 X NC_000023.11:g.43741895C>T
GRCh37.p13 chr X NC_000023.10:g.43601142C>T
MAOA RefSeqGene NG_008957.2:g.90735C>T
Gene: MAOA, monoamine oxidase A (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MAOA transcript variant 1 NM_000240.4:c.1165-55C>T N/A Intron Variant
MAOA transcript variant 2 NM_001270458.2:c.766-55C>T 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 C= T
GRCh38.p14 chr X NC_000023.11:g.43741895= NC_000023.11:g.43741895C>T
GRCh37.p13 chr X NC_000023.10:g.43601142= NC_000023.10:g.43601142C>T
MAOA RefSeqGene NG_008957.2:g.90735= NG_008957.2:g.90735C>T
MAOA transcript variant 1 NM_000240.3:c.1165-55= NM_000240.3:c.1165-55C>T
MAOA transcript variant 1 NM_000240.4:c.1165-55= NM_000240.4:c.1165-55C>T
MAOA transcript variant 2 NM_001270458.1:c.766-55= NM_001270458.1:c.766-55C>T
MAOA transcript variant 2 NM_001270458.2:c.766-55= NM_001270458.2:c.766-55C>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#.

112 SubSNP, 16 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss1432445 Oct 05, 2000 (86)
2 YUSUKE ss2986855 Jun 15, 2001 (96)
3 HGBASE ss3187802 Aug 15, 2001 (98)
4 ACEVAN ss4258333 Jan 04, 2002 (102)
5 SC_SNP ss8237893 Apr 21, 2003 (114)
6 SC_SNP ss8488471 Jul 11, 2003 (116)
7 SC_SNP ss15973529 Feb 27, 2004 (120)
8 CSHL-HAPMAP ss19822855 Feb 27, 2004 (120)
9 SSAHASNP ss21038445 Apr 05, 2004 (121)
10 PERLEGEN ss24227255 Sep 20, 2004 (123)
11 ILLUMINA ss75097037 Dec 06, 2007 (129)
12 AFFY ss76425210 Dec 08, 2007 (130)
13 CGM_KYOTO ss76876402 Dec 06, 2007 (129)
14 SI_EXO ss76883843 Dec 06, 2007 (129)
15 HGSV ss83875173 Dec 15, 2007 (130)
16 SHGC ss99307777 Feb 06, 2009 (130)
17 1000GENOMES ss112871405 Jan 25, 2009 (130)
18 1000GENOMES ss114663232 Jan 25, 2009 (130)
19 ILLUMINA-UK ss115611384 Feb 06, 2009 (130)
20 KRIBB_YJKIM ss119376543 Dec 01, 2009 (131)
21 ENSEMBL ss133970550 Dec 01, 2009 (131)
22 ILLUMINA ss161012215 Dec 01, 2009 (131)
23 COMPLETE_GENOMICS ss163098995 Jul 04, 2010 (132)
24 COMPLETE_GENOMICS ss164832299 Jul 04, 2010 (132)
25 COMPLETE_GENOMICS ss166214119 Jul 04, 2010 (132)
26 ILLUMINA ss174897425 Jul 04, 2010 (132)
27 BUSHMAN ss204225397 Jul 04, 2010 (132)
28 BCM-HGSC-SUB ss208867960 Jul 04, 2010 (132)
29 BL ss255983088 May 09, 2011 (134)
30 GMI ss283741994 May 04, 2012 (137)
31 GMI ss287608632 Apr 25, 2013 (138)
32 PJP ss294548271 May 09, 2011 (134)
33 1000GENOMES ss341453378 May 09, 2011 (134)
34 ILLUMINA ss481977452 May 04, 2012 (137)
35 ILLUMINA ss482011102 May 04, 2012 (137)
36 ILLUMINA ss482964711 Sep 08, 2015 (146)
37 ILLUMINA ss485782209 May 04, 2012 (137)
38 ILLUMINA ss537627530 Sep 08, 2015 (146)
39 TISHKOFF ss566850888 Apr 25, 2013 (138)
40 SSMP ss662785070 Apr 25, 2013 (138)
41 ILLUMINA ss778647183 Sep 08, 2015 (146)
42 ILLUMINA ss783336974 Sep 08, 2015 (146)
43 ILLUMINA ss784288488 Sep 08, 2015 (146)
44 ILLUMINA ss832598792 Sep 08, 2015 (146)
45 ILLUMINA ss834104975 Sep 08, 2015 (146)
46 JMKIDD_LAB ss1082896730 Aug 21, 2014 (142)
47 DDI ss1432035336 Apr 01, 2015 (144)
48 1000GENOMES ss1554248664 Apr 01, 2015 (144)
49 EVA_GENOME_DK ss1583381658 Apr 01, 2015 (144)
50 EVA_UK10K_ALSPAC ss1640681638 Apr 01, 2015 (144)
51 EVA_UK10K_TWINSUK ss1683675671 Apr 01, 2015 (144)
52 EVA_MGP ss1711580321 Apr 01, 2015 (144)
53 ILLUMINA ss1752807003 Sep 08, 2015 (146)
54 WEILL_CORNELL_DGM ss1939306045 Feb 12, 2016 (147)
55 GENOMED ss1971372809 Jul 19, 2016 (147)
56 USC_VALOUEV ss2159035117 Dec 20, 2016 (150)
57 HUMAN_LONGEVITY ss2317050654 Dec 20, 2016 (150)
58 SYSTEMSBIOZJU ss2629696784 Nov 08, 2017 (151)
59 ILLUMINA ss2634957226 Nov 08, 2017 (151)
60 GRF ss2710156833 Nov 08, 2017 (151)
61 GNOMAD ss2978334279 Nov 08, 2017 (151)
62 AFFY ss2986130256 Nov 08, 2017 (151)
63 SWEGEN ss3019897393 Nov 08, 2017 (151)
64 BIOINF_KMB_FNS_UNIBA ss3029042117 Nov 08, 2017 (151)
65 ILLUMINA ss3630426607 Oct 12, 2018 (152)
66 ILLUMINA ss3632843579 Oct 12, 2018 (152)
67 ILLUMINA ss3633557928 Oct 12, 2018 (152)
68 ILLUMINA ss3634287678 Oct 12, 2018 (152)
69 ILLUMINA ss3635247830 Oct 12, 2018 (152)
70 ILLUMINA ss3635965032 Oct 12, 2018 (152)
71 ILLUMINA ss3636996390 Oct 12, 2018 (152)
72 ILLUMINA ss3637718498 Oct 12, 2018 (152)
73 ILLUMINA ss3638856348 Oct 12, 2018 (152)
74 ILLUMINA ss3640955313 Oct 12, 2018 (152)
75 ILLUMINA ss3641255091 Oct 12, 2018 (152)
76 ILLUMINA ss3641553143 Oct 12, 2018 (152)
77 ILLUMINA ss3643780652 Oct 12, 2018 (152)
78 OMUKHERJEE_ADBS ss3646572038 Oct 12, 2018 (152)
79 URBANLAB ss3651269114 Oct 12, 2018 (152)
80 ILLUMINA ss3654250621 Oct 12, 2018 (152)
81 ILLUMINA ss3745548249 Jul 13, 2019 (153)
82 EVA ss3770116799 Jul 13, 2019 (153)
83 ILLUMINA ss3773039953 Jul 13, 2019 (153)
84 PACBIO ss3788894524 Jul 13, 2019 (153)
85 PACBIO ss3793758580 Jul 13, 2019 (153)
86 PACBIO ss3798643656 Jul 13, 2019 (153)
87 KHV_HUMAN_GENOMES ss3822948514 Jul 13, 2019 (153)
88 EVA ss3825977397 Apr 27, 2020 (154)
89 EVA ss3836157991 Apr 27, 2020 (154)
90 EVA ss3841692098 Apr 27, 2020 (154)
91 EVA ss3847211242 Apr 27, 2020 (154)
92 SGDP_PRJ ss3891343702 Apr 27, 2020 (154)
93 KRGDB ss3941746611 Apr 27, 2020 (154)
94 FSA-LAB ss3984440251 Apr 26, 2021 (155)
95 EVA ss3984765384 Apr 26, 2021 (155)
96 EVA ss3986876437 Apr 26, 2021 (155)
97 TOPMED ss5121348954 Apr 26, 2021 (155)
98 TOMMO_GENOMICS ss5234267154 Apr 26, 2021 (155)
99 1000G_HIGH_COVERAGE ss5312393562 Oct 16, 2022 (156)
100 EVA ss5316082186 Oct 16, 2022 (156)
101 HUGCELL_USP ss5504080355 Oct 16, 2022 (156)
102 1000G_HIGH_COVERAGE ss5620547646 Oct 16, 2022 (156)
103 EVA ss5623984798 Oct 16, 2022 (156)
104 EVA ss5624191327 Oct 16, 2022 (156)
105 SANFORD_IMAGENETICS ss5665161536 Oct 16, 2022 (156)
106 TOMMO_GENOMICS ss5795913292 Oct 16, 2022 (156)
107 EVA ss5800238573 Oct 16, 2022 (156)
108 YY_MCH ss5819013984 Oct 16, 2022 (156)
109 EVA ss5848741162 Oct 16, 2022 (156)
110 EVA ss5857070939 Oct 16, 2022 (156)
111 EVA ss5978162587 Oct 16, 2022 (156)
112 EVA ss5981155241 Oct 16, 2022 (156)
113 1000Genomes NC_000023.10 - 43601142 Oct 12, 2018 (152)
114 1000Genomes_30x NC_000023.11 - 43741895 Oct 16, 2022 (156)
115 The Avon Longitudinal Study of Parents and Children NC_000023.10 - 43601142 Oct 12, 2018 (152)
116 The Danish reference pan genome NC_000023.10 - 43601142 Apr 27, 2020 (154)
117 HapMap NC_000023.11 - 43741895 Apr 27, 2020 (154)
118 KOREAN population from KRGDB NC_000023.10 - 43601142 Apr 27, 2020 (154)
119 Medical Genome Project healthy controls from Spanish population NC_000023.10 - 43601142 Apr 27, 2020 (154)
120 Qatari NC_000023.10 - 43601142 Apr 27, 2020 (154)
121 SGDP_PRJ NC_000023.10 - 43601142 Apr 27, 2020 (154)
122 Siberian NC_000023.10 - 43601142 Apr 27, 2020 (154)
123 8.3KJPN NC_000023.10 - 43601142 Apr 26, 2021 (155)
124 14KJPN NC_000023.11 - 43741895 Oct 16, 2022 (156)
125 TopMed NC_000023.11 - 43741895 Apr 26, 2021 (155)
126 UK 10K study - Twins NC_000023.10 - 43601142 Oct 12, 2018 (152)
127 A Vietnamese Genetic Variation Database NC_000023.10 - 43601142 Jul 13, 2019 (153)
128 ALFA NC_000023.11 - 43741895 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)
rs17244885 Oct 07, 2004 (123)
rs56504459 May 26, 2008 (130)
rs60574103 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss83875173 NC_000023.8:43357395:C:T NC_000023.11:43741894:C:T (self)
ss112871405, ss114663232, ss115611384, ss163098995, ss164832299, ss166214119, ss204225397, ss208867960, ss255983088, ss283741994, ss287608632, ss294548271, ss481977452, ss3643780652 NC_000023.9:43486085:C:T NC_000023.11:43741894:C:T (self)
82225429, 45404794, 9546595, 48924005, 696081, 21347967, 43360682, 11551471, 92236461, 45404794, 10008403, ss341453378, ss482011102, ss482964711, ss485782209, ss537627530, ss566850888, ss662785070, ss778647183, ss783336974, ss784288488, ss832598792, ss834104975, ss1082896730, ss1432035336, ss1554248664, ss1583381658, ss1640681638, ss1683675671, ss1711580321, ss1752807003, ss1939306045, ss1971372809, ss2159035117, ss2629696784, ss2634957226, ss2710156833, ss2978334279, ss2986130256, ss3019897393, ss3630426607, ss3632843579, ss3633557928, ss3634287678, ss3635247830, ss3635965032, ss3636996390, ss3637718498, ss3638856348, ss3640955313, ss3641255091, ss3641553143, ss3646572038, ss3654250621, ss3745548249, ss3770116799, ss3773039953, ss3788894524, ss3793758580, ss3798643656, ss3825977397, ss3836157991, ss3841692098, ss3891343702, ss3941746611, ss3984440251, ss3984765384, ss3986876437, ss5234267154, ss5316082186, ss5623984798, ss5624191327, ss5665161536, ss5800238573, ss5848741162, ss5978162587, ss5981155241 NC_000023.10:43601141:C:T NC_000023.11:43741894:C:T (self)
108073581, 3978211, 129750396, 684955311, 7557334795, ss2317050654, ss3029042117, ss3651269114, ss3822948514, ss3847211242, ss5121348954, ss5312393562, ss5504080355, ss5620547646, ss5795913292, ss5819013984, ss5857070939 NC_000023.11:43741894:C:T NC_000023.11:43741894:C:T (self)
ss8488471 NT_011568.12:6421009:C:T NC_000023.11:43741894:C:T (self)
ss15973529, ss19822855, ss21038445 NT_011568.13:10531:C:T NC_000023.11:43741894:C:T (self)
ss76883843 NT_079573.3:6452908:C:T NC_000023.11:43741894:C:T (self)
ss1432445, ss2986855, ss3187802, ss4258333, ss8237893, ss24227255, ss75097037, ss76425210, ss76876402, ss99307777, ss119376543, ss133970550, ss161012215, ss174897425 NT_079573.4:6452885:C:T NC_000023.11:43741894: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.

10 citations for rs979606
PMID Title Author Year Journal
16848906 Genetic polymorphisms in monoamine neurotransmitter systems show only weak association with acute post-surgical pain in humans. Kim H et al. 2006 Molecular pain
19018232 Comparison of the genotyping results using DNA obtained from blood and saliva. Philibert RA et al. 2008 Psychiatric genetics
19693267 Financial and psychological risk attitudes associated with two single nucleotide polymorphisms in the nicotine receptor (CHRNA4) gene. Roe BE et al. 2009 PloS one
19772600 A comparison of classification methods for predicting Chronic Fatigue Syndrome based on genetic data. Huang LC et al. 2009 Journal of translational medicine
21445666 Family-based association analysis of alcohol dependence in the COGA sample and replication in the Australian twin-family study. Wang KS et al. 2011 Journal of neural transmission (Vienna, Austria
22552845 XM: association testing on the X-chromosome in case-control samples with related individuals. Thornton T et al. 2012 Genetic epidemiology
22832821 Working memory brain activity and capacity link MAOA polymorphism to aggressive behavior during development. Ziermans T et al. 2012 Translational psychiatry
27521242 TPH-2 Polymorphisms Interact with Early Life Stress to Influence Response to Treatment with Antidepressant Drugs. Xu Z et al. 2016 The international journal of neuropsychopharmacology
29075213 Monoamine Oxidase A (MAOA) Gene and Personality Traits from Late Adolescence through Early Adulthood: A Latent Variable Investigation. Xu MK et al. 2017 Frontiers in psychology
31129315 Systematic Review and Meta-Analysis of Genetic Risk of Developing Chronic Postsurgical Pain. Chidambaran V et al. 2020 The journal of pain
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