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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.

rs4135307

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr3:12361041 (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
A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.022268 (5894/264690, TOPMED)
G=0.002909 (382/131300, ALFA)
G=0.03343 (2631/78700, PAGE_STUDY) (+ 10 more)
G=0.0222 (142/6404, 1000G_30x)
G=0.0204 (102/5008, 1000G)
T=0.0002 (1/4480, Estonian)
G=0.0003 (1/3854, ALSPAC)
G=0.0000 (0/3708, TWINSUK)
G=0.068 (67/982, HapMap)
G=0.014 (3/216, Qatari)
G=0.06 (5/90, PharmGKB)
A=0.50 (7/14, SGDP_PRJ)
G=0.50 (7/14, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PPARG : Intron Variant
Publications
0 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 131300 A=0.997083 G=0.002909, T=0.000008
European Sub 115118 A=0.999835 G=0.000156, T=0.000009
African Sub 6792 A=0.9563 G=0.0437, T=0.0000
African Others Sub 230 A=0.970 G=0.030, T=0.000
African American Sub 6562 A=0.9558 G=0.0442, T=0.0000
Asian Sub 656 A=1.000 G=0.000, T=0.000
East Asian Sub 524 A=1.000 G=0.000, T=0.000
Other Asian Sub 132 A=1.000 G=0.000, T=0.000
Latin American 1 Sub 664 A=0.982 G=0.018, T=0.000
Latin American 2 Sub 2210 A=0.9973 G=0.0027, T=0.0000
South Asian Sub 190 A=1.000 G=0.000, T=0.000
Other Sub 5670 A=0.9914 G=0.0086, T=0.0000


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 A=0.977732 G=0.022268
Allele Frequency Aggregator Total Global 131300 A=0.997083 G=0.002909, T=0.000008
Allele Frequency Aggregator European Sub 115118 A=0.999835 G=0.000156, T=0.000009
Allele Frequency Aggregator African Sub 6792 A=0.9563 G=0.0437, T=0.0000
Allele Frequency Aggregator Other Sub 5670 A=0.9914 G=0.0086, T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 2210 A=0.9973 G=0.0027, T=0.0000
Allele Frequency Aggregator Latin American 1 Sub 664 A=0.982 G=0.018, T=0.000
Allele Frequency Aggregator Asian Sub 656 A=1.000 G=0.000, T=0.000
Allele Frequency Aggregator South Asian Sub 190 A=1.000 G=0.000, T=0.000
The PAGE Study Global Study-wide 78700 A=0.96657 G=0.03343
The PAGE Study AfricanAmerican Sub 32514 A=0.93480 G=0.06520
The PAGE Study Mexican Sub 10810 A=0.99759 G=0.00241
The PAGE Study Asian Sub 8318 A=0.9999 G=0.0001
The PAGE Study PuertoRican Sub 7918 A=0.9749 G=0.0251
The PAGE Study NativeHawaiian Sub 4534 A=0.9976 G=0.0024
The PAGE Study Cuban Sub 4230 A=0.9884 G=0.0116
The PAGE Study Dominican Sub 3828 A=0.9545 G=0.0455
The PAGE Study CentralAmerican Sub 2450 A=0.9861 G=0.0139
The PAGE Study SouthAmerican Sub 1982 A=0.9965 G=0.0035
The PAGE Study NativeAmerican Sub 1260 A=0.9921 G=0.0079
The PAGE Study SouthAsian Sub 856 A=1.000 G=0.000
1000Genomes_30x Global Study-wide 6404 A=0.9778 G=0.0222
1000Genomes_30x African Sub 1786 A=0.9255 G=0.0745
1000Genomes_30x Europe Sub 1266 A=1.0000 G=0.0000
1000Genomes_30x South Asian Sub 1202 A=1.0000 G=0.0000
1000Genomes_30x East Asian Sub 1170 A=1.0000 G=0.0000
1000Genomes_30x American Sub 980 A=0.991 G=0.009
1000Genomes Global Study-wide 5008 A=0.9796 G=0.0204
1000Genomes African Sub 1322 A=0.9281 G=0.0719
1000Genomes East Asian Sub 1008 A=1.0000 G=0.0000
1000Genomes Europe Sub 1006 A=1.0000 G=0.0000
1000Genomes South Asian Sub 978 A=1.000 G=0.000
1000Genomes American Sub 694 A=0.990 G=0.010
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.9998 T=0.0002
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.9997 G=0.0003
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=1.0000 G=0.0000
HapMap Global Study-wide 982 A=0.932 G=0.068
HapMap African Sub 692 A=0.918 G=0.082
HapMap American Sub 204 A=0.956 G=0.044
HapMap Asian Sub 86 A=0.99 G=0.01
Qatari Global Study-wide 216 A=0.986 G=0.014
PharmGKB Aggregated Global Study-wide 90 A=0.94 G=0.06
PharmGKB Aggregated PA130227878 Sub 90 A=0.94 G=0.06
SGDP_PRJ Global Study-wide 14 A=0.50 G=0.50
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 3 NC_000003.12:g.12361041A>G
GRCh38.p14 chr 3 NC_000003.12:g.12361041A>T
GRCh37.p13 chr 3 NC_000003.11:g.12402540A>G
GRCh37.p13 chr 3 NC_000003.11:g.12402540A>T
PPARG RefSeqGene NG_011749.1:g.78192A>G
PPARG RefSeqGene NG_011749.1:g.78192A>T
Gene: PPARG, peroxisome proliferator activated receptor gamma (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PPARG transcript variant 5 NM_001330615.4:c.-8-18663…

NM_001330615.4:c.-8-18663A>G

N/A Intron Variant
PPARG transcript variant 6 NM_001354666.3:c.-8-18663…

NM_001354666.3:c.-8-18663A>G

N/A Intron Variant
PPARG transcript variant 7 NM_001354667.3:c.-8-18663…

NM_001354667.3:c.-8-18663A>G

N/A Intron Variant
PPARG transcript variant 8 NM_001354668.2:c.82+9367A…

NM_001354668.2:c.82+9367A>G

N/A Intron Variant
PPARG transcript variant 9 NM_001354669.2:c.-435-186…

NM_001354669.2:c.-435-18663A>G

N/A Intron Variant
PPARG transcript variant 10 NM_001354670.2:c.-2-18663…

NM_001354670.2:c.-2-18663A>G

N/A Intron Variant
PPARG transcript variant 11 NM_001374261.3:c.-8-18663…

NM_001374261.3:c.-8-18663A>G

N/A Intron Variant
PPARG transcript variant 12 NM_001374262.3:c.-9+16147…

NM_001374262.3:c.-9+16147A>G

N/A Intron Variant
PPARG transcript variant 13 NM_001374263.2:c.-8-18663…

NM_001374263.2:c.-8-18663A>G

N/A Intron Variant
PPARG transcript variant 14 NM_001374264.2:c.-8-18663…

NM_001374264.2:c.-8-18663A>G

N/A Intron Variant
PPARG transcript variant 15 NM_001374265.1:c.82+9367A…

NM_001374265.1:c.82+9367A>G

N/A Intron Variant
PPARG transcript variant 16 NM_001374266.1:c.-2-18663…

NM_001374266.1:c.-2-18663A>G

N/A Intron Variant
PPARG transcript variant 4 NM_005037.7:c.-8-18663A>G N/A Intron Variant
PPARG transcript variant 2 NM_015869.5:c.82+9367A>G N/A Intron Variant
PPARG transcript variant 3 NM_138711.6:c.-8-18663A>G N/A Intron Variant
PPARG transcript variant 1 NM_138712.5:c.-8-18663A>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 A= G T
GRCh38.p14 chr 3 NC_000003.12:g.12361041= NC_000003.12:g.12361041A>G NC_000003.12:g.12361041A>T
GRCh37.p13 chr 3 NC_000003.11:g.12402540= NC_000003.11:g.12402540A>G NC_000003.11:g.12402540A>T
PPARG RefSeqGene NG_011749.1:g.78192= NG_011749.1:g.78192A>G NG_011749.1:g.78192A>T
PPARG transcript variant 5 NM_001330615.4:c.-8-18663= NM_001330615.4:c.-8-18663A>G NM_001330615.4:c.-8-18663A>T
PPARG transcript variant 6 NM_001354666.3:c.-8-18663= NM_001354666.3:c.-8-18663A>G NM_001354666.3:c.-8-18663A>T
PPARG transcript variant 7 NM_001354667.3:c.-8-18663= NM_001354667.3:c.-8-18663A>G NM_001354667.3:c.-8-18663A>T
PPARG transcript variant 8 NM_001354668.2:c.82+9367= NM_001354668.2:c.82+9367A>G NM_001354668.2:c.82+9367A>T
PPARG transcript variant 9 NM_001354669.2:c.-435-18663= NM_001354669.2:c.-435-18663A>G NM_001354669.2:c.-435-18663A>T
PPARG transcript variant 10 NM_001354670.2:c.-2-18663= NM_001354670.2:c.-2-18663A>G NM_001354670.2:c.-2-18663A>T
PPARG transcript variant 11 NM_001374261.3:c.-8-18663= NM_001374261.3:c.-8-18663A>G NM_001374261.3:c.-8-18663A>T
PPARG transcript variant 12 NM_001374262.3:c.-9+16147= NM_001374262.3:c.-9+16147A>G NM_001374262.3:c.-9+16147A>T
PPARG transcript variant 13 NM_001374263.2:c.-8-18663= NM_001374263.2:c.-8-18663A>G NM_001374263.2:c.-8-18663A>T
PPARG transcript variant 14 NM_001374264.2:c.-8-18663= NM_001374264.2:c.-8-18663A>G NM_001374264.2:c.-8-18663A>T
PPARG transcript variant 15 NM_001374265.1:c.82+9367= NM_001374265.1:c.82+9367A>G NM_001374265.1:c.82+9367A>T
PPARG transcript variant 16 NM_001374266.1:c.-2-18663= NM_001374266.1:c.-2-18663A>G NM_001374266.1:c.-2-18663A>T
PPARG transcript variant 4 NM_005037.5:c.-2-18663= NM_005037.5:c.-2-18663A>G NM_005037.5:c.-2-18663A>T
PPARG transcript variant 4 NM_005037.7:c.-8-18663= NM_005037.7:c.-8-18663A>G NM_005037.7:c.-8-18663A>T
PPARG transcript variant 2 NM_015869.4:c.82+9367= NM_015869.4:c.82+9367A>G NM_015869.4:c.82+9367A>T
PPARG transcript variant 2 NM_015869.5:c.82+9367= NM_015869.5:c.82+9367A>G NM_015869.5:c.82+9367A>T
PPARG transcript variant 3 NM_138711.3:c.-2-18663= NM_138711.3:c.-2-18663A>G NM_138711.3:c.-2-18663A>T
PPARG transcript variant 3 NM_138711.6:c.-8-18663= NM_138711.6:c.-8-18663A>G NM_138711.6:c.-8-18663A>T
PPARG transcript variant 1 NM_138712.3:c.-2-18663= NM_138712.3:c.-2-18663A>G NM_138712.3:c.-2-18663A>T
PPARG transcript variant 1 NM_138712.5:c.-8-18663= NM_138712.5:c.-8-18663A>G NM_138712.5:c.-8-18663A>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#.

60 SubSNP, 14 Frequency submissions
No Submitter Submission ID Date (Build)
1 PGA-UW-FHCRC ss5587638 Oct 10, 2002 (108)
2 BCM_SSAHASNP ss14197202 Dec 05, 2003 (119)
3 PARC ss23143937 Sep 20, 2004 (126)
4 PGA-UW-FHCRC ss28447561 Sep 21, 2004 (123)
5 PHARMGKB_PARC ss69365013 May 18, 2007 (127)
6 ILLUMINA ss75248407 Dec 06, 2007 (129)
7 KRIBB_YJKIM ss119470650 Dec 01, 2009 (131)
8 ILLUMINA ss160662850 Dec 01, 2009 (131)
9 ILLUMINA ss173689827 Jul 04, 2010 (132)
10 BUSHMAN ss202147051 Jul 04, 2010 (132)
11 1000GENOMES ss219984734 Jul 14, 2010 (132)
12 ILLUMINA ss480893997 May 04, 2012 (137)
13 ILLUMINA ss480912839 May 04, 2012 (137)
14 ILLUMINA ss481865987 Sep 08, 2015 (146)
15 ILLUMINA ss485242020 May 04, 2012 (137)
16 ILLUMINA ss537215902 Sep 08, 2015 (146)
17 TISHKOFF ss556431024 Apr 25, 2013 (138)
18 ILLUMINA ss778902778 Sep 08, 2015 (146)
19 ILLUMINA ss783066948 Sep 08, 2015 (146)
20 ILLUMINA ss784024869 Sep 08, 2015 (146)
21 ILLUMINA ss832325009 Sep 08, 2015 (146)
22 ILLUMINA ss834364046 Sep 08, 2015 (146)
23 1000GENOMES ss1302833720 Aug 21, 2014 (142)
24 EVA_UK10K_ALSPAC ss1606431175 Apr 01, 2015 (144)
25 EVA_UK10K_TWINSUK ss1649425208 Apr 01, 2015 (144)
26 ILLUMINA ss1752436659 Sep 08, 2015 (146)
27 HAMMER_LAB ss1798870738 Sep 08, 2015 (146)
28 WEILL_CORNELL_DGM ss1921532655 Feb 12, 2016 (147)
29 ILLUMINA ss1958537947 Feb 12, 2016 (147)
30 HUMAN_LONGEVITY ss2249137693 Dec 20, 2016 (150)
31 ILLUMINA ss2633912639 Nov 08, 2017 (151)
32 GNOMAD ss2789618955 Nov 08, 2017 (151)
33 ILLUMINA ss3022212461 Nov 08, 2017 (151)
34 ILLUMINA ss3628592089 Oct 11, 2018 (152)
35 ILLUMINA ss3631861149 Oct 11, 2018 (152)
36 ILLUMINA ss3633282359 Oct 11, 2018 (152)
37 ILLUMINA ss3633998848 Oct 11, 2018 (152)
38 ILLUMINA ss3634880728 Oct 11, 2018 (152)
39 ILLUMINA ss3635683032 Oct 11, 2018 (152)
40 ILLUMINA ss3636576903 Oct 11, 2018 (152)
41 ILLUMINA ss3637435336 Oct 11, 2018 (152)
42 ILLUMINA ss3638397649 Oct 11, 2018 (152)
43 ILLUMINA ss3640588031 Oct 11, 2018 (152)
44 ILLUMINA ss3643355943 Oct 11, 2018 (152)
45 ILLUMINA ss3652678589 Oct 11, 2018 (152)
46 EGCUT_WGS ss3659742146 Jul 13, 2019 (153)
47 ILLUMINA ss3725990884 Jul 13, 2019 (153)
48 ILLUMINA ss3745180532 Jul 13, 2019 (153)
49 PAGE_CC ss3771011314 Jul 13, 2019 (153)
50 ILLUMINA ss3772676318 Jul 13, 2019 (153)
51 KHV_HUMAN_GENOMES ss3802820271 Jul 13, 2019 (153)
52 SGDP_PRJ ss3855243087 Apr 25, 2020 (154)
53 TOPMED ss4554467905 Apr 27, 2021 (155)
54 1000G_HIGH_COVERAGE ss5253075356 Oct 13, 2022 (156)
55 EVA ss5337941693 Oct 13, 2022 (156)
56 HUGCELL_USP ss5452573573 Oct 13, 2022 (156)
57 1000G_HIGH_COVERAGE ss5530920573 Oct 13, 2022 (156)
58 SANFORD_IMAGENETICS ss5631557497 Oct 13, 2022 (156)
59 EVA ss5867660883 Oct 13, 2022 (156)
60 EVA ss5959817505 Oct 13, 2022 (156)
61 1000Genomes NC_000003.11 - 12402540 Oct 11, 2018 (152)
62 1000Genomes_30x NC_000003.12 - 12361041 Oct 13, 2022 (156)
63 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 12402540 Oct 11, 2018 (152)
64 Genetic variation in the Estonian population NC_000003.11 - 12402540 Oct 11, 2018 (152)
65 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 99254163 (NC_000003.12:12361040:A:G 2875/140192)
Row 99254164 (NC_000003.12:12361040:A:T 1/140200)

- Apr 27, 2021 (155)
66 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 99254163 (NC_000003.12:12361040:A:G 2875/140192)
Row 99254164 (NC_000003.12:12361040:A:T 1/140200)

- Apr 27, 2021 (155)
67 HapMap NC_000003.12 - 12361041 Apr 25, 2020 (154)
68 The PAGE Study NC_000003.12 - 12361041 Jul 13, 2019 (153)
69 PharmGKB Aggregated NC_000003.12 - 12361041 Apr 25, 2020 (154)
70 Qatari NC_000003.11 - 12402540 Apr 25, 2020 (154)
71 SGDP_PRJ NC_000003.11 - 12402540 Apr 25, 2020 (154)
72 TopMed NC_000003.12 - 12361041 Apr 27, 2021 (155)
73 UK 10K study - Twins NC_000003.11 - 12402540 Oct 11, 2018 (152)
74 ALFA NC_000003.12 - 12361041 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)
rs17241139 Mar 10, 2006 (126)
rs17838662 Oct 07, 2004 (123)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss202147051, ss480893997, ss3643355943 NC_000003.10:12377539:A:G NC_000003.12:12361040:A:G (self)
13979699, 7749865, 3574585, 7260067, 7749865, ss219984734, ss480912839, ss481865987, ss485242020, ss537215902, ss556431024, ss778902778, ss783066948, ss784024869, ss832325009, ss834364046, ss1302833720, ss1606431175, ss1649425208, ss1752436659, ss1798870738, ss1921532655, ss1958537947, ss2633912639, ss2789618955, ss3022212461, ss3628592089, ss3631861149, ss3633282359, ss3633998848, ss3634880728, ss3635683032, ss3636576903, ss3637435336, ss3638397649, ss3640588031, ss3652678589, ss3745180532, ss3772676318, ss3855243087, ss5337941693, ss5631557497, ss5959817505 NC_000003.11:12402539:A:G NC_000003.12:12361040:A:G (self)
18446508, 2304375, 232783, 7914, 391845460, 8844930438, ss2249137693, ss3725990884, ss3771011314, ss3802820271, ss4554467905, ss5253075356, ss5452573573, ss5530920573, ss5867660883 NC_000003.12:12361040:A:G NC_000003.12:12361040:A:G (self)
ss14197202 NT_022517.16:12342539:A:G NC_000003.12:12361040:A:G (self)
ss5587638, ss23143937, ss28447561, ss69365013, ss75248407, ss119470650, ss160662850, ss173689827 NT_022517.18:12342539:A:G NC_000003.12:12361040:A:G (self)
5480394, ss2789618955, ss3659742146 NC_000003.11:12402539:A:T NC_000003.12:12361040:A:T (self)
8844930438 NC_000003.12:12361040:A:T NC_000003.12:12361040:A:T (self)
Help

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

No publications for rs4135307

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