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dbSNP Short Genetic Variations

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.

rs6413419

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr10:133532171 (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
G>A / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.03319 (8172/246218, GnomAD)
A=0.07786 (9777/125568, TOPMED)
A=0.03635 (4411/121352, ExAC) (+ 6 more)
A=0.0737 (2277/30904, GnomAD)
A=0.0865 (1125/13006, GO-ESP)
A=0.077 (388/5008, 1000G)
A=0.019 (87/4480, Estonian)
A=0.021 (82/3854, ALSPAC)
A=0.019 (71/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CYP2E1 : Missense Variant
Publications
4 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 10 NC_000010.11:g.133532171G>A
GRCh38.p12 chr 10 NC_000010.11:g.133532171G>T
GRCh37.p13 chr 10 NC_000010.10:g.135345675G>A
GRCh37.p13 chr 10 NC_000010.10:g.135345675G>T
CYP2E1 RefSeqGene NG_008383.1:g.9809G>A
CYP2E1 RefSeqGene NG_008383.1:g.9809G>T
Gene: CYP2E1, cytochrome P450 family 2 subfamily E member 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CYP2E1 transcript NM_000773.3:c.535G>A V [GTC] > I [ATC] Coding Sequence Variant
cytochrome P450 2E1 precursor NP_000764.1:p.Val179Ile V (Val) > I (Ile) Missense Variant
CYP2E1 transcript NM_000773.3:c.535G>T V [GTC] > F [TTC] Coding Sequence Variant
cytochrome P450 2E1 precursor NP_000764.1:p.Val179Phe V (Val) > F (Phe) Missense 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
gnomAD - Exomes Global Study-wide 246218 G=0.96681 A=0.03319, T=0.00000
gnomAD - Exomes European Sub 133986 G=0.97678 A=0.02321, T=0.00001
gnomAD - Exomes Asian Sub 48022 G=0.9877 A=0.0123, T=0.0000
gnomAD - Exomes American Sub 33582 G=0.9759 A=0.0241, T=0.0000
gnomAD - Exomes African Sub 15298 G=0.7955 A=0.2045, T=0.0000
gnomAD - Exomes Ashkenazi Jewish Sub 9848 G=0.966 A=0.034, T=0.000
gnomAD - Exomes Other Sub 5482 G=0.963 A=0.037, T=0.000
TopMed Global Study-wide 125568 G=0.92214 A=0.07786
ExAC Global Study-wide 121352 G=0.96365 A=0.03635
ExAC Europe Sub 73310 G=0.9772 A=0.0228
ExAC Asian Sub 25158 G=0.9874 A=0.0126
ExAC American Sub 11578 G=0.9777 A=0.0223
ExAC African Sub 10398 G=0.7954 A=0.2046
ExAC Other Sub 908 G=0.96 A=0.04
gnomAD - Genomes Global Study-wide 30904 G=0.9263 A=0.0737
gnomAD - Genomes European Sub 18476 G=0.9788 A=0.0212
gnomAD - Genomes African Sub 8688 G=0.792 A=0.208
gnomAD - Genomes East Asian Sub 1618 G=1.000 A=0.000
gnomAD - Genomes Other Sub 982 G=0.97 A=0.03
gnomAD - Genomes American Sub 838 G=0.96 A=0.04
gnomAD - Genomes Ashkenazi Jewish Sub 302 G=0.97 A=0.03
GO Exome Sequencing Project Global Study-wide 13006 G=0.9135 A=0.0865
GO Exome Sequencing Project European American Sub 8600 G=0.974 A=0.026
GO Exome Sequencing Project African American Sub 4406 G=0.795 A=0.205
1000Genomes Global Study-wide 5008 G=0.923 A=0.077
1000Genomes African Sub 1322 G=0.762 A=0.238
1000Genomes East Asian Sub 1008 G=1.000 A=0.000
1000Genomes Europe Sub 1006 G=0.969 A=0.031
1000Genomes South Asian Sub 978 G=0.99 A=0.01
1000Genomes American Sub 694 G=0.96 A=0.04
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.981 A=0.019
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.979 A=0.021
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.981 A=0.019
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 G= A T Note
GRCh38.p12 chr 10 NC_000010.11:g.13...

NC_000010.11:g.133532171G=

NC_000010.11:g.13...

NC_000010.11:g.133532171G>A

NC_000010.11:g.13...

NC_000010.11:g.133532171G>T

GRCh37.p13 chr 10 NC_000010.10:g.13...

NC_000010.10:g.135345675G=

NC_000010.10:g.13...

NC_000010.10:g.135345675G>A

NC_000010.10:g.13...

NC_000010.10:g.135345675G>T

CYP2E1 RefSeqGene NG_008383.1:g.9809G= NG_008383.1:g.980...

NG_008383.1:g.9809G>A

NG_008383.1:g.980...

NG_008383.1:g.9809G>T

CYP2E1 transcript NM_000773.3:c.535G= NM_000773.3:c.535G>A NM_000773.3:c.535G>T
cytochrome P450 2E1 precursor NP_000764.1:p.Val...

NP_000764.1:p.Val179=

NP_000764.1:p.Val...

NP_000764.1:p.Val179Ile

NP_000764.1:p.Val...

NP_000764.1:p.Val179Phe

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#.

96 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 SNP500CANCER ss5586441 Jul 02, 2003 (116)
2 BCM_SSAHASNP ss14252506 Dec 05, 2003 (119)
3 SC_SNP ss15577727 Feb 27, 2004 (120)
4 PERLEGEN ss23588573 Sep 20, 2004 (123)
5 BIOVENTURES ss32476088 May 24, 2005 (125)
6 PERLEGEN ss69097801 May 17, 2007 (127)
7 ILLUMINA ss74887579 Dec 06, 2007 (129)
8 CGM_KYOTO ss76860216 Dec 06, 2007 (129)
9 CCHMC-CAE-PGCORE ss79314194 Dec 15, 2007 (130)
10 PHARMGKB_AB_DME ss84155492 Dec 15, 2007 (130)
11 CNG ss95212385 Mar 25, 2008 (129)
12 1000GENOMES ss114071253 Jan 25, 2009 (130)
13 KRIBB_YJKIM ss119509330 Dec 01, 2009 (131)
14 ILLUMINA ss154357525 Dec 01, 2009 (131)
15 ILLUMINA ss159533784 Dec 01, 2009 (131)
16 SEATTLESEQ ss159721864 Dec 01, 2009 (131)
17 ILLUMINA ss160771128 Dec 01, 2009 (131)
18 COMPLETE_GENOMICS ss171460856 Jul 04, 2010 (132)
19 ILLUMINA ss173995361 Jul 04, 2010 (132)
20 BUSHMAN ss202249183 Jul 04, 2010 (132)
21 1000GENOMES ss225041801 Jul 14, 2010 (132)
22 1000GENOMES ss235407878 Jul 15, 2010 (132)
23 ILLUMINA ss244304757 Jul 04, 2010 (132)
24 PJP ss290971426 May 09, 2011 (134)
25 NHLBI-ESP ss342312859 May 09, 2011 (134)
26 ILLUMINA ss481233437 May 04, 2012 (137)
27 ILLUMINA ss481257050 May 04, 2012 (137)
28 ILLUMINA ss482243258 Sep 08, 2015 (146)
29 ILLUMINA ss485412078 May 04, 2012 (137)
30 1000GENOMES ss491008309 May 04, 2012 (137)
31 EXOME_CHIP ss491442845 May 04, 2012 (137)
32 CLINSEQ_SNP ss491635354 May 04, 2012 (137)
33 ILLUMINA ss537345853 Sep 08, 2015 (146)
34 TISHKOFF ss562324975 Apr 25, 2013 (138)
35 SSMP ss657634210 Apr 25, 2013 (138)
36 ILLUMINA ss778567206 Sep 08, 2015 (146)
37 ILLUMINA ss780892322 Sep 08, 2015 (146)
38 ILLUMINA ss783151485 Sep 08, 2015 (146)
39 ILLUMINA ss783578782 Sep 08, 2015 (146)
40 ILLUMINA ss784107436 Sep 08, 2015 (146)
41 ILLUMINA ss832410695 Sep 08, 2015 (146)
42 ILLUMINA ss834024189 Sep 08, 2015 (146)
43 JMKIDD_LAB ss974476969 Aug 21, 2014 (142)
44 EVA-GONL ss988110260 Aug 21, 2014 (142)
45 JMKIDD_LAB ss1067517862 Aug 21, 2014 (142)
46 JMKIDD_LAB ss1077434973 Aug 21, 2014 (142)
47 1000GENOMES ss1339759451 Aug 21, 2014 (142)
48 HAMMER_LAB ss1397597301 Sep 08, 2015 (146)
49 EVA_FINRISK ss1584071494 Apr 01, 2015 (144)
50 EVA_DECODE ss1597789227 Apr 01, 2015 (144)
51 EVA_UK10K_ALSPAC ss1625813071 Apr 01, 2015 (144)
52 EVA_UK10K_TWINSUK ss1668807104 Apr 01, 2015 (144)
53 EVA_EXAC ss1690153077 Apr 01, 2015 (144)
54 EVA_MGP ss1711275959 Apr 01, 2015 (144)
55 EVA_SVP ss1713226197 Apr 01, 2015 (144)
56 ILLUMINA ss1751957717 Sep 08, 2015 (146)
57 ILLUMINA ss1751957718 Sep 08, 2015 (146)
58 ILLUMINA ss1917853464 Feb 12, 2016 (147)
59 WEILL_CORNELL_DGM ss1931468897 Feb 12, 2016 (147)
60 ILLUMINA ss1946297986 Feb 12, 2016 (147)
61 ILLUMINA ss1959312207 Feb 12, 2016 (147)
62 JJLAB ss2026475077 Sep 14, 2016 (149)
63 USC_VALOUEV ss2154758261 Dec 20, 2016 (150)
64 HUMAN_LONGEVITY ss2179510885 Dec 20, 2016 (150)
65 TOPMED ss2342623925 Dec 20, 2016 (150)
66 ILLUMINA ss2632788407 Nov 08, 2017 (151)
67 ILLUMINA ss2632788408 Nov 08, 2017 (151)
68 ILLUMINA ss2635021926 Nov 08, 2017 (151)
69 ILLUMINA ss2710726251 Nov 08, 2017 (151)
70 GNOMAD ss2738638706 Nov 08, 2017 (151)
71 GNOMAD ss2748507438 Nov 08, 2017 (151)
72 GNOMAD ss2895306391 Nov 08, 2017 (151)
73 AFFY ss2984928964 Nov 08, 2017 (151)
74 AFFY ss2985576246 Nov 08, 2017 (151)
75 SWEGEN ss3007433603 Nov 08, 2017 (151)
76 ILLUMINA ss3021294549 Nov 08, 2017 (151)
77 CSIRBIOHTS ss3029638125 Nov 08, 2017 (151)
78 TOPMED ss3134813764 Nov 08, 2017 (151)
79 CSHL ss3349401366 Nov 08, 2017 (151)
80 ILLUMINA ss3626577471 Oct 12, 2018 (152)
81 ILLUMINA ss3626577472 Oct 12, 2018 (152)
82 ILLUMINA ss3630809023 Oct 12, 2018 (152)
83 ILLUMINA ss3632971900 Oct 12, 2018 (152)
84 ILLUMINA ss3633670229 Oct 12, 2018 (152)
85 ILLUMINA ss3634433578 Oct 12, 2018 (152)
86 ILLUMINA ss3634433579 Oct 12, 2018 (152)
87 ILLUMINA ss3635362212 Oct 12, 2018 (152)
88 ILLUMINA ss3636118842 Oct 12, 2018 (152)
89 ILLUMINA ss3637112987 Oct 12, 2018 (152)
90 ILLUMINA ss3637884843 Oct 12, 2018 (152)
91 ILLUMINA ss3640140919 Oct 12, 2018 (152)
92 ILLUMINA ss3640140920 Oct 12, 2018 (152)
93 ILLUMINA ss3642885221 Oct 12, 2018 (152)
94 ILLUMINA ss3644550761 Oct 12, 2018 (152)
95 ILLUMINA ss3651654794 Oct 12, 2018 (152)
96 ILLUMINA ss3653700445 Oct 12, 2018 (152)
97 1000Genomes NC_000010.10 - 135345675 Oct 12, 2018 (152)
98 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 135345675 Oct 12, 2018 (152)
99 Genetic variation in the Estonian population NC_000010.10 - 135345675 Oct 12, 2018 (152)
100 ExAC NC_000010.10 - 135345675 Oct 12, 2018 (152)
101 gnomAD - Genomes NC_000010.10 - 135345675 Oct 12, 2018 (152)
102 gnomAD - Exomes NC_000010.10 - 135345675 Oct 12, 2018 (152)
103 GO Exome Sequencing Project NC_000010.10 - 135345675 Oct 12, 2018 (152)
104 TopMed NC_000010.11 - 133532171 Oct 12, 2018 (152)
105 UK 10K study - Twins NC_000010.10 - 135345675 Oct 12, 2018 (152)
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)
rs60363119 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss114071253, ss171460856, ss202249183, ss290971426, ss481233437, ss491635354, ss1397597301, ss1597789227, ss1713226197, ss2635021926, ss3642885221 NC_000010.9:135195664:G= NC_000010.11:133532170:G= (self)
52230144, 29022067, 20589535, 393131, 29007912, 6212612, 1029129, 29022067, ss225041801, ss235407878, ss342312859, ss481257050, ss482243258, ss485412078, ss491008309, ss491442845, ss537345853, ss562324975, ss657634210, ss778567206, ss780892322, ss783151485, ss783578782, ss784107436, ss832410695, ss834024189, ss974476969, ss988110260, ss1067517862, ss1077434973, ss1339759451, ss1584071494, ss1625813071, ss1668807104, ss1690153077, ss1711275959, ss1751957717, ss1751957718, ss1917853464, ss1931468897, ss1946297986, ss1959312207, ss2026475077, ss2154758261, ss2342623925, ss2632788407, ss2632788408, ss2710726251, ss2738638706, ss2748507438, ss2895306391, ss2984928964, ss2985576246, ss3007433603, ss3021294549, ss3029638125, ss3349401366, ss3626577471, ss3626577472, ss3630809023, ss3632971900, ss3633670229, ss3634433578, ss3634433579, ss3635362212, ss3636118842, ss3637112987, ss3637884843, ss3640140919, ss3640140920, ss3644550761, ss3651654794, ss3653700445 NC_000010.10:135345674:G= NC_000010.11:133532170:G= (self)
55169605, ss2179510885, ss3134813764 NC_000010.11:133532170:G= NC_000010.11:133532170:G= (self)
ss5586441, ss23588573, ss32476088, ss69097801, ss74887579, ss76860216, ss79314194, ss84155492, ss95212385, ss119509330, ss154357525, ss159533784, ss159721864, ss160771128, ss173995361, ss244304757 NT_008818.16:6579605:G= NC_000010.11:133532170:G= (self)
ss14252506, ss15577727 NT_017795.16:501253:G= NC_000010.11:133532170:G= (self)
ss114071253, ss171460856, ss202249183, ss290971426, ss481233437, ss491635354, ss1397597301, ss1597789227, ss1713226197, ss2635021926, ss3642885221 NC_000010.9:135195664:G>A NC_000010.11:133532170:G>A (self)
52230144, 29022067, 20589535, 393131, 29007912, 6212612, 1029129, 29022067, ss225041801, ss235407878, ss342312859, ss481257050, ss482243258, ss485412078, ss491008309, ss491442845, ss537345853, ss562324975, ss657634210, ss778567206, ss780892322, ss783151485, ss783578782, ss784107436, ss832410695, ss834024189, ss974476969, ss988110260, ss1067517862, ss1077434973, ss1339759451, ss1584071494, ss1625813071, ss1668807104, ss1690153077, ss1711275959, ss1751957717, ss1751957718, ss1917853464, ss1931468897, ss1946297986, ss1959312207, ss2026475077, ss2154758261, ss2342623925, ss2632788407, ss2632788408, ss2710726251, ss2738638706, ss2748507438, ss2895306391, ss2984928964, ss2985576246, ss3007433603, ss3021294549, ss3029638125, ss3349401366, ss3626577471, ss3626577472, ss3630809023, ss3632971900, ss3633670229, ss3634433578, ss3634433579, ss3635362212, ss3636118842, ss3637112987, ss3637884843, ss3640140919, ss3640140920, ss3644550761, ss3651654794, ss3653700445 NC_000010.10:135345674:G>A NC_000010.11:133532170:G>A (self)
55169605, ss2179510885, ss3134813764 NC_000010.11:133532170:G>A NC_000010.11:133532170:G>A (self)
ss5586441, ss23588573, ss32476088, ss69097801, ss74887579, ss76860216, ss79314194, ss84155492, ss95212385, ss119509330, ss154357525, ss159533784, ss159721864, ss160771128, ss173995361, ss244304757 NT_008818.16:6579605:G>A NC_000010.11:133532170:G>A (self)
ss14252506, ss15577727 NT_017795.16:501253:G>A NC_000010.11:133532170:G>A (self)
6212612, ss2738638706 NC_000010.10:135345674:G>T NC_000010.11:133532170:G>T (self)
Help

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

4 citations for rs6413419
PMID Title Author Year Journal
18663376 Global patterns of variation in allele and haplotype frequencies and linkage disequilibrium across the CYP2E1 gene. Lee MY et al. 2008 The pharmacogenomics journal
19131562 Biomarkers of human exposure to acrylamide and relation to polymorphisms in metabolizing genes. Duale N et al. 2009 Toxicological sciences
22560290 A comparison of Val81Met and other polymorphisms of alcohol metabolising genes in patients and controls in Northern Spain. Celorrio D et al. 2012 Alcohol (Fayetteville, N.Y.)
25419409 CYP2E1 gene rs6413420 polymorphism was first found in the Bouyei ethnic group of China. Liu W et al. 2014 International journal of clinical and experimental medicine

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.post76+b4aec9c