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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.

rs2886161

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr2:177263111 (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 / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.292546 (77434/264690, TOPMED)
C=0.288846 (40476/140130, GnomAD)
T=0.41446 (11711/28256, 14KJPN) (+ 18 more)
T=0.41289 (6920/16760, 8.3KJPN)
C=0.19605 (2622/13374, ALFA)
C=0.3709 (2375/6404, 1000G_30x)
C=0.3764 (1885/5008, 1000G)
C=0.3415 (1530/4480, Estonian)
C=0.3223 (1242/3854, ALSPAC)
C=0.3188 (1182/3708, TWINSUK)
T=0.4437 (1300/2930, KOREAN)
T=0.4471 (819/1832, Korea1K)
C=0.329 (328/998, GoNL)
C=0.497 (390/784, PRJEB37584)
C=0.243 (146/600, NorthernSweden)
T=0.336 (113/336, SGDP_PRJ)
C=0.317 (104/328, HapMap)
C=0.417 (90/216, Qatari)
T=0.403 (87/216, Vietnamese)
C=0.17 (7/40, GENOME_DK)
T=0.30 (12/40, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
NFE2L2 : Intron Variant
Publications
4 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 13374 T=0.80395 C=0.19605, G=0.00000
European Sub 10474 T=0.76637 C=0.23363, G=0.00000
African Sub 2162 T=0.9505 C=0.0495, G=0.0000
African Others Sub 90 T=0.94 C=0.06, G=0.00
African American Sub 2072 T=0.9508 C=0.0492, G=0.0000
Asian Sub 20 T=0.90 C=0.10, G=0.00
East Asian Sub 16 T=1.00 C=0.00, G=0.00
Other Asian Sub 4 T=0.5 C=0.5, G=0.0
Latin American 1 Sub 72 T=1.00 C=0.00, G=0.00
Latin American 2 Sub 164 T=1.000 C=0.000, G=0.000
South Asian Sub 30 T=0.97 C=0.03, G=0.00
Other Sub 452 T=0.856 C=0.144, G=0.000


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=0.707454 C=0.292546
gnomAD - Genomes Global Study-wide 140130 T=0.711154 C=0.288846
gnomAD - Genomes European Sub 75856 T=0.67919 C=0.32081
gnomAD - Genomes African Sub 42020 T=0.81873 C=0.18127
gnomAD - Genomes American Sub 13650 T=0.59883 C=0.40117
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=0.7440 C=0.2560
gnomAD - Genomes East Asian Sub 3128 T=0.4984 C=0.5016
gnomAD - Genomes Other Sub 2152 T=0.7082 C=0.2918
14KJPN JAPANESE Study-wide 28256 T=0.41446 C=0.58554
8.3KJPN JAPANESE Study-wide 16760 T=0.41289 C=0.58711
Allele Frequency Aggregator Total Global 13374 T=0.80395 C=0.19605, G=0.00000
Allele Frequency Aggregator European Sub 10474 T=0.76637 C=0.23363, G=0.00000
Allele Frequency Aggregator African Sub 2162 T=0.9505 C=0.0495, G=0.0000
Allele Frequency Aggregator Other Sub 452 T=0.856 C=0.144, G=0.000
Allele Frequency Aggregator Latin American 2 Sub 164 T=1.000 C=0.000, G=0.000
Allele Frequency Aggregator Latin American 1 Sub 72 T=1.00 C=0.00, G=0.00
Allele Frequency Aggregator South Asian Sub 30 T=0.97 C=0.03, G=0.00
Allele Frequency Aggregator Asian Sub 20 T=0.90 C=0.10, G=0.00
1000Genomes_30x Global Study-wide 6404 T=0.6291 C=0.3709
1000Genomes_30x African Sub 1786 T=0.8527 C=0.1473
1000Genomes_30x Europe Sub 1266 T=0.6927 C=0.3073
1000Genomes_30x South Asian Sub 1202 T=0.4443 C=0.5557
1000Genomes_30x East Asian Sub 1170 T=0.4530 C=0.5470
1000Genomes_30x American Sub 980 T=0.577 C=0.423
1000Genomes Global Study-wide 5008 T=0.6236 C=0.3764
1000Genomes African Sub 1322 T=0.8548 C=0.1452
1000Genomes East Asian Sub 1008 T=0.4474 C=0.5526
1000Genomes Europe Sub 1006 T=0.6918 C=0.3082
1000Genomes South Asian Sub 978 T=0.458 C=0.542
1000Genomes American Sub 694 T=0.573 C=0.427
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.6585 C=0.3415
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.6777 C=0.3223
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.6812 C=0.3188
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.4437 C=0.5563, G=0.0000
Korean Genome Project KOREAN Study-wide 1832 T=0.4471 C=0.5529
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.671 C=0.329
CNV burdens in cranial meningiomas Global Study-wide 784 T=0.503 C=0.497
CNV burdens in cranial meningiomas CRM Sub 784 T=0.503 C=0.497
Northern Sweden ACPOP Study-wide 600 T=0.757 C=0.243
SGDP_PRJ Global Study-wide 336 T=0.336 C=0.664
HapMap Global Study-wide 328 T=0.683 C=0.317
HapMap African Sub 120 T=0.800 C=0.200
HapMap American Sub 120 T=0.700 C=0.300
HapMap Asian Sub 88 T=0.50 C=0.50
Qatari Global Study-wide 216 T=0.583 C=0.417
A Vietnamese Genetic Variation Database Global Study-wide 216 T=0.403 C=0.597
The Danish reference pan genome Danish Study-wide 40 T=0.82 C=0.17
Siberian Global Study-wide 40 T=0.30 C=0.70
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 2 NC_000002.12:g.177263111T>C
GRCh38.p14 chr 2 NC_000002.12:g.177263111T>G
GRCh37.p13 chr 2 NC_000002.11:g.178127839T>C
GRCh37.p13 chr 2 NC_000002.11:g.178127839T>G
LOC126806417 genomic region NG_082737.1:g.511T>C
LOC126806417 genomic region NG_082737.1:g.511T>G
Gene: NFE2L2, NFE2 like bZIP transcription factor 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
NFE2L2 transcript variant 2 NM_001145412.3:c.-4+292A>G N/A Intron Variant
NFE2L2 transcript variant 3 NM_001145413.3:c.-4+292A>G N/A Intron Variant
NFE2L2 transcript variant 4 NM_001313900.1:c.-4+418A>G N/A Intron Variant
NFE2L2 transcript variant 5 NM_001313901.1:c.-4+326A>G N/A Intron Variant
NFE2L2 transcript variant 6 NM_001313902.2:c.45+1421A…

NM_001313902.2:c.45+1421A>G

N/A Intron Variant
NFE2L2 transcript variant 7 NM_001313903.2:c.45+1421A…

NM_001313903.2:c.45+1421A>G

N/A Intron Variant
NFE2L2 transcript variant 8 NM_001313904.1:c.-185+292…

NM_001313904.1:c.-185+292A>G

N/A Intron Variant
NFE2L2 transcript variant 1 NM_006164.5:c.45+1421A>G 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 G
GRCh38.p14 chr 2 NC_000002.12:g.177263111= NC_000002.12:g.177263111T>C NC_000002.12:g.177263111T>G
GRCh37.p13 chr 2 NC_000002.11:g.178127839= NC_000002.11:g.178127839T>C NC_000002.11:g.178127839T>G
LOC126806417 genomic region NG_082737.1:g.511= NG_082737.1:g.511T>C NG_082737.1:g.511T>G
NFE2L2 transcript variant 2 NM_001145412.2:c.-4+292= NM_001145412.2:c.-4+292A>G NM_001145412.2:c.-4+292A>C
NFE2L2 transcript variant 2 NM_001145412.3:c.-4+292= NM_001145412.3:c.-4+292A>G NM_001145412.3:c.-4+292A>C
NFE2L2 transcript variant 3 NM_001145413.2:c.-4+292= NM_001145413.2:c.-4+292A>G NM_001145413.2:c.-4+292A>C
NFE2L2 transcript variant 3 NM_001145413.3:c.-4+292= NM_001145413.3:c.-4+292A>G NM_001145413.3:c.-4+292A>C
NFE2L2 transcript variant 4 NM_001313900.1:c.-4+418= NM_001313900.1:c.-4+418A>G NM_001313900.1:c.-4+418A>C
NFE2L2 transcript variant 5 NM_001313901.1:c.-4+326= NM_001313901.1:c.-4+326A>G NM_001313901.1:c.-4+326A>C
NFE2L2 transcript variant 6 NM_001313902.2:c.45+1421= NM_001313902.2:c.45+1421A>G NM_001313902.2:c.45+1421A>C
NFE2L2 transcript variant 7 NM_001313903.2:c.45+1421= NM_001313903.2:c.45+1421A>G NM_001313903.2:c.45+1421A>C
NFE2L2 transcript variant 8 NM_001313904.1:c.-185+292= NM_001313904.1:c.-185+292A>G NM_001313904.1:c.-185+292A>C
NFE2L2 transcript variant 1 NM_006164.4:c.45+1421= NM_006164.4:c.45+1421A>G NM_006164.4:c.45+1421A>C
NFE2L2 transcript variant 1 NM_006164.5:c.45+1421= NM_006164.5:c.45+1421A>G NM_006164.5:c.45+1421A>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#.

66 SubSNP, 21 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss4078116 Nov 05, 2001 (101)
2 WI_SSAHASNP ss11447004 Jul 11, 2003 (116)
3 ABI ss44183250 Mar 14, 2006 (126)
4 PERLEGEN ss68836500 May 18, 2007 (127)
5 BGI ss106142075 Feb 04, 2009 (130)
6 1000GENOMES ss111323846 Jan 25, 2009 (130)
7 ILLUMINA-UK ss117988058 Feb 14, 2009 (130)
8 ENSEMBL ss132878507 Dec 01, 2009 (131)
9 GMI ss158023997 Dec 01, 2009 (131)
10 COMPLETE_GENOMICS ss164942306 Jul 04, 2010 (132)
11 BCM-HGSC-SUB ss205823259 Jul 04, 2010 (132)
12 1000GENOMES ss219675197 Jul 14, 2010 (132)
13 1000GENOMES ss231485356 Jul 14, 2010 (132)
14 1000GENOMES ss238970645 Jul 15, 2010 (132)
15 GMI ss276803131 May 04, 2012 (137)
16 TISHKOFF ss556061561 Apr 25, 2013 (138)
17 SSMP ss649717225 Apr 25, 2013 (138)
18 EVA-GONL ss977686894 Aug 21, 2014 (142)
19 JMKIDD_LAB ss1069737025 Aug 21, 2014 (142)
20 1000GENOMES ss1300584463 Aug 21, 2014 (142)
21 DDI ss1428833950 Apr 01, 2015 (144)
22 EVA_GENOME_DK ss1579215441 Apr 01, 2015 (144)
23 EVA_DECODE ss1587127377 Apr 01, 2015 (144)
24 EVA_UK10K_ALSPAC ss1605232669 Apr 01, 2015 (144)
25 EVA_UK10K_TWINSUK ss1648226702 Apr 01, 2015 (144)
26 HAMMER_LAB ss1797972319 Sep 08, 2015 (146)
27 WEILL_CORNELL_DGM ss1920937705 Feb 12, 2016 (147)
28 GENOMED ss1968962269 Jul 19, 2016 (147)
29 JJLAB ss2021006041 Sep 14, 2016 (149)
30 USC_VALOUEV ss2149072482 Dec 20, 2016 (150)
31 HUMAN_LONGEVITY ss2236903030 Dec 20, 2016 (150)
32 SYSTEMSBIOZJU ss2625006322 Nov 08, 2017 (151)
33 GRF ss2703711866 Nov 08, 2017 (151)
34 GNOMAD ss2783265515 Nov 08, 2017 (151)
35 SWEGEN ss2990930758 Nov 08, 2017 (151)
36 BIOINF_KMB_FNS_UNIBA ss3024263489 Nov 08, 2017 (151)
37 CSHL ss3344624466 Nov 08, 2017 (151)
38 URBANLAB ss3647216248 Oct 11, 2018 (152)
39 EGCUT_WGS ss3658805317 Jul 13, 2019 (153)
40 EVA_DECODE ss3705504183 Jul 13, 2019 (153)
41 ACPOP ss3729143289 Jul 13, 2019 (153)
42 EVA ss3757769650 Jul 13, 2019 (153)
43 PACBIO ss3784079074 Jul 13, 2019 (153)
44 PACBIO ss3789629059 Jul 13, 2019 (153)
45 PACBIO ss3794502137 Jul 13, 2019 (153)
46 KHV_HUMAN_GENOMES ss3802127930 Jul 13, 2019 (153)
47 EVA ss3827374339 Apr 25, 2020 (154)
48 EVA ss3837105643 Apr 25, 2020 (154)
49 EVA ss3842525842 Apr 25, 2020 (154)
50 SGDP_PRJ ss3854057758 Apr 25, 2020 (154)
51 KRGDB ss3899703445 Apr 25, 2020 (154)
52 KOGIC ss3949579997 Apr 25, 2020 (154)
53 EVA ss3984494178 Apr 26, 2021 (155)
54 TOPMED ss4535112908 Apr 26, 2021 (155)
55 TOMMO_GENOMICS ss5155299337 Apr 26, 2021 (155)
56 1000G_HIGH_COVERAGE ss5251107017 Oct 12, 2022 (156)
57 HUGCELL_USP ss5450815452 Oct 12, 2022 (156)
58 EVA ss5506701832 Oct 12, 2022 (156)
59 1000G_HIGH_COVERAGE ss5527960452 Oct 12, 2022 (156)
60 SANFORD_IMAGENETICS ss5630433783 Oct 12, 2022 (156)
61 TOMMO_GENOMICS ss5685835739 Oct 12, 2022 (156)
62 YY_MCH ss5803001075 Oct 12, 2022 (156)
63 EVA ss5821233464 Oct 12, 2022 (156)
64 EVA ss5852849040 Oct 12, 2022 (156)
65 EVA ss5933639486 Oct 12, 2022 (156)
66 EVA ss5956664195 Oct 12, 2022 (156)
67 1000Genomes NC_000002.11 - 178127839 Oct 11, 2018 (152)
68 1000Genomes_30x NC_000002.12 - 177263111 Oct 12, 2022 (156)
69 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 178127839 Oct 11, 2018 (152)
70 Genetic variation in the Estonian population NC_000002.11 - 178127839 Oct 11, 2018 (152)
71 The Danish reference pan genome NC_000002.11 - 178127839 Apr 25, 2020 (154)
72 gnomAD - Genomes NC_000002.12 - 177263111 Apr 26, 2021 (155)
73 Genome of the Netherlands Release 5 NC_000002.11 - 178127839 Apr 25, 2020 (154)
74 HapMap NC_000002.12 - 177263111 Apr 25, 2020 (154)
75 KOREAN population from KRGDB NC_000002.11 - 178127839 Apr 25, 2020 (154)
76 Korean Genome Project NC_000002.12 - 177263111 Apr 25, 2020 (154)
77 Northern Sweden NC_000002.11 - 178127839 Jul 13, 2019 (153)
78 CNV burdens in cranial meningiomas NC_000002.11 - 178127839 Apr 26, 2021 (155)
79 Qatari NC_000002.11 - 178127839 Apr 25, 2020 (154)
80 SGDP_PRJ NC_000002.11 - 178127839 Apr 25, 2020 (154)
81 Siberian NC_000002.11 - 178127839 Apr 25, 2020 (154)
82 8.3KJPN NC_000002.11 - 178127839 Apr 26, 2021 (155)
83 14KJPN NC_000002.12 - 177263111 Oct 12, 2022 (156)
84 TopMed NC_000002.12 - 177263111 Apr 26, 2021 (155)
85 UK 10K study - Twins NC_000002.11 - 178127839 Oct 11, 2018 (152)
86 A Vietnamese Genetic Variation Database NC_000002.11 - 178127839 Jul 13, 2019 (153)
87 ALFA NC_000002.12 - 177263111 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss111323846, ss117988058, ss164942306, ss205823259, ss276803131, ss1587127377 NC_000002.10:177836084:T:C NC_000002.12:177263110:T:C (self)
11648306, 6433047, 4543565, 5380380, 2826034, 6880839, 2428154, 43513, 2979635, 6074738, 1588836, 13268644, 6433047, 1399860, ss219675197, ss231485356, ss238970645, ss556061561, ss649717225, ss977686894, ss1069737025, ss1300584463, ss1428833950, ss1579215441, ss1605232669, ss1648226702, ss1797972319, ss1920937705, ss1968962269, ss2021006041, ss2149072482, ss2625006322, ss2703711866, ss2783265515, ss2990930758, ss3344624466, ss3658805317, ss3729143289, ss3757769650, ss3784079074, ss3789629059, ss3794502137, ss3827374339, ss3837105643, ss3854057758, ss3899703445, ss3984494178, ss5155299337, ss5506701832, ss5630433783, ss5821233464, ss5956664195 NC_000002.11:178127838:T:C NC_000002.12:177263110:T:C (self)
15486387, 83020722, 1957235, 5957998, 19672843, 338935787, 15182220721, ss2236903030, ss3024263489, ss3647216248, ss3705504183, ss3802127930, ss3842525842, ss3949579997, ss4535112908, ss5251107017, ss5450815452, ss5527960452, ss5685835739, ss5803001075, ss5852849040, ss5933639486 NC_000002.12:177263110:T:C NC_000002.12:177263110:T:C (self)
ss11447004 NT_005403.13:28287176:T:C NC_000002.12:177263110:T:C (self)
ss4078116, ss44183250, ss68836500, ss106142075, ss132878507, ss158023997 NT_005403.17:28337256:T:C NC_000002.12:177263110:T:C (self)
6880839, ss3899703445 NC_000002.11:178127838:T:G NC_000002.12:177263110:T:G (self)
15182220721 NC_000002.12:177263110:T:G NC_000002.12:177263110:T:G (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 rs2886161
PMID Title Author Year Journal
20196834 Association of Nrf2-encoding NFE2L2 haplotypes with Parkinson's disease. von Otter M et al. 2010 BMC medical genetics
28253266 Association of OGG1 and MTHFR polymorphisms with age-related cataract: A systematic review and meta-analysis. Wu X et al. 2017 PloS one
31586142 Association between genetic polymorphisms of NRF2, KEAP1, MAFF, MAFK and anti-tuberculosis drug-induced liver injury: a nested case-control study. Chen S et al. 2019 Scientific reports
33096746 Genetic Landscape of Common Epilepsies: Advancing towards Precision in Treatment. Thakran S et al. 2020 International journal of molecular sciences
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