Name: rs4135318
Published: September 21, 2022
License: Open Access

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.

rs4135318

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr3:12374554 (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: G>A
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.130643 (34580/264690, TOPMED)
A=0.124804 (17474/140012, GnomAD)
A=0.00007 (2/28258, 14KJPN) (+ 11 more)
A=0.06871 (1298/18890, ALFA)
A=0.00006 (1/16760, 8.3KJPN)
A=0.1362 (872/6404, 1000G_30x)
A=0.1276 (639/5008, 1000G)
A=0.0007 (3/4480, Estonian)
A=0.0026 (10/3854, ALSPAC)
A=0.0013 (5/3708, TWINSUK)
A=0.002 (2/998, GoNL)
A=0.093 (20/216, Qatari)
A=0.191 (36/188, PharmGKB)
G=0.36 (16/44, 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	18890	G=0.93129	A=0.06871
European	Sub	14286	G=0.99769	A=0.00231
African	Sub	2946	G=0.6093	A=0.3907
African Others	Sub	114	G=0.579	A=0.421
African American	Sub	2832	G=0.6105	A=0.3895
Asian	Sub	112	G=1.000	A=0.000
East Asian	Sub	86	G=1.00	A=0.00
Other Asian	Sub	26	G=1.00	A=0.00
Latin American 1	Sub	146	G=0.918	A=0.082
Latin American 2	Sub	610	G=0.969	A=0.031
South Asian	Sub	98	G=1.00	A=0.00
Other	Sub	692	G=0.880	A=0.120

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	G=0.869357	A=0.130643
gnomAD - Genomes	Global	Study-wide	140012	G=0.875196	A=0.124804
gnomAD - Genomes	European	Sub	75888	G=0.99794	A=0.00206
gnomAD - Genomes	African	Sub	41888	G=0.60755	A=0.39245
gnomAD - Genomes	American	Sub	13634	G=0.95181	A=0.04819
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	G=0.9955	A=0.0045
gnomAD - Genomes	East Asian	Sub	3130	G=1.0000	A=0.0000
gnomAD - Genomes	Other	Sub	2152	G=0.9038	A=0.0962
14KJPN	JAPANESE	Study-wide	28258	G=0.99993	A=0.00007
Allele Frequency Aggregator	Total	Global	18890	G=0.93129	A=0.06871
Allele Frequency Aggregator	European	Sub	14286	G=0.99769	A=0.00231
Allele Frequency Aggregator	African	Sub	2946	G=0.6093	A=0.3907
Allele Frequency Aggregator	Other	Sub	692	G=0.880	A=0.120
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.969	A=0.031
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.918	A=0.082
Allele Frequency Aggregator	Asian	Sub	112	G=1.000	A=0.000
Allele Frequency Aggregator	South Asian	Sub	98	G=1.00	A=0.00
8.3KJPN	JAPANESE	Study-wide	16760	G=0.99994	A=0.00006
1000Genomes_30x	Global	Study-wide	6404	G=0.8638	A=0.1362
1000Genomes_30x	African	Sub	1786	G=0.5370	A=0.4630
1000Genomes_30x	Europe	Sub	1266	G=1.0000	A=0.0000
1000Genomes_30x	South Asian	Sub	1202	G=1.0000	A=0.0000
1000Genomes_30x	East Asian	Sub	1170	G=1.0000	A=0.0000
1000Genomes_30x	American	Sub	980	G=0.954	A=0.046
1000Genomes	Global	Study-wide	5008	G=0.8724	A=0.1276
1000Genomes	African	Sub	1322	G=0.5424	A=0.4576
1000Genomes	East Asian	Sub	1008	G=1.0000	A=0.0000
1000Genomes	Europe	Sub	1006	G=1.0000	A=0.0000
1000Genomes	South Asian	Sub	978	G=1.000	A=0.000
1000Genomes	American	Sub	694	G=0.951	A=0.049
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.9993	A=0.0007
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.9974	A=0.0026
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.9987	A=0.0013
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.998	A=0.002
Qatari	Global	Study-wide	216	G=0.907	A=0.093
PharmGKB Aggregated	Global	Study-wide	188	G=0.809	A=0.191
PharmGKB Aggregated	PA130216758	Sub	94	G=0.81	A=0.19
PharmGKB Aggregated	PA130217040	Sub	94	G=0.81	A=0.19
SGDP_PRJ	Global	Study-wide	44	G=0.36	A=0.64

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.12374554G>A
GRCh37.p13 chr 3	NC_000003.11:g.12416053G>A
PPARG RefSeqGene	NG_011749.1:g.91705G>A

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.-8-5150G… NM_001330615.4:c.-8-5150G>A	N/A	Intron Variant
PPARG transcript variant 6	NM_001354666.3:c.-8-5150G… NM_001354666.3:c.-8-5150G>A	N/A	Intron Variant
PPARG transcript variant 7	NM_001354667.3:c.-8-5150G… NM_001354667.3:c.-8-5150G>A	N/A	Intron Variant
PPARG transcript variant 8	NM_001354668.2:c.83-5150G… NM_001354668.2:c.83-5150G>A	N/A	Intron Variant
PPARG transcript variant 9	NM_001354669.2:c.-435-515… NM_001354669.2:c.-435-5150G>A	N/A	Intron Variant
PPARG transcript variant 10	NM_001354670.2:c.-2-5150G… NM_001354670.2:c.-2-5150G>A	N/A	Intron Variant
PPARG transcript variant 11	NM_001374261.3:c.-8-5150G… NM_001374261.3:c.-8-5150G>A	N/A	Intron Variant
PPARG transcript variant 12	NM_001374262.3:c.-8-5150G… NM_001374262.3:c.-8-5150G>A	N/A	Intron Variant
PPARG transcript variant 13	NM_001374263.2:c.-8-5150G… NM_001374263.2:c.-8-5150G>A	N/A	Intron Variant
PPARG transcript variant 14	NM_001374264.2:c.-8-5150G… NM_001374264.2:c.-8-5150G>A	N/A	Intron Variant
PPARG transcript variant 15	NM_001374265.1:c.83-5150G… NM_001374265.1:c.83-5150G>A	N/A	Intron Variant
PPARG transcript variant 16	NM_001374266.1:c.-2-5150G… NM_001374266.1:c.-2-5150G>A	N/A	Intron Variant
PPARG transcript variant 4	NM_005037.7:c.-8-5150G>A	N/A	Intron Variant
PPARG transcript variant 2	NM_015869.5:c.83-5150G>A	N/A	Intron Variant
PPARG transcript variant 3	NM_138711.6:c.-8-5150G>A	N/A	Intron Variant
PPARG transcript variant 1	NM_138712.5:c.-8-5150G>A	N/A	Intron Variant

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

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
GRCh38.p14 chr 3	NC_000003.12:g.12374554=	NC_000003.12:g.12374554G>A
GRCh37.p13 chr 3	NC_000003.11:g.12416053=	NC_000003.11:g.12416053G>A
PPARG RefSeqGene	NG_011749.1:g.91705=	NG_011749.1:g.91705G>A
PPARG transcript variant 5	NM_001330615.4:c.-8-5150=	NM_001330615.4:c.-8-5150G>A
PPARG transcript variant 6	NM_001354666.3:c.-8-5150=	NM_001354666.3:c.-8-5150G>A
PPARG transcript variant 7	NM_001354667.3:c.-8-5150=	NM_001354667.3:c.-8-5150G>A
PPARG transcript variant 8	NM_001354668.2:c.83-5150=	NM_001354668.2:c.83-5150G>A
PPARG transcript variant 9	NM_001354669.2:c.-435-5150=	NM_001354669.2:c.-435-5150G>A
PPARG transcript variant 10	NM_001354670.2:c.-2-5150=	NM_001354670.2:c.-2-5150G>A
PPARG transcript variant 11	NM_001374261.3:c.-8-5150=	NM_001374261.3:c.-8-5150G>A
PPARG transcript variant 12	NM_001374262.3:c.-8-5150=	NM_001374262.3:c.-8-5150G>A
PPARG transcript variant 13	NM_001374263.2:c.-8-5150=	NM_001374263.2:c.-8-5150G>A
PPARG transcript variant 14	NM_001374264.2:c.-8-5150=	NM_001374264.2:c.-8-5150G>A
PPARG transcript variant 15	NM_001374265.1:c.83-5150=	NM_001374265.1:c.83-5150G>A
PPARG transcript variant 16	NM_001374266.1:c.-2-5150=	NM_001374266.1:c.-2-5150G>A
PPARG transcript variant 4	NM_005037.5:c.-2-5150=	NM_005037.5:c.-2-5150G>A
PPARG transcript variant 4	NM_005037.7:c.-8-5150=	NM_005037.7:c.-8-5150G>A
PPARG transcript variant 2	NM_015869.4:c.83-5150=	NM_015869.4:c.83-5150G>A
PPARG transcript variant 2	NM_015869.5:c.83-5150=	NM_015869.5:c.83-5150G>A
PPARG transcript variant 3	NM_138711.3:c.-2-5150=	NM_138711.3:c.-2-5150G>A
PPARG transcript variant 3	NM_138711.6:c.-8-5150=	NM_138711.6:c.-8-5150G>A
PPARG transcript variant 1	NM_138712.3:c.-2-5150=	NM_138712.3:c.-2-5150G>A
PPARG transcript variant 1	NM_138712.5:c.-8-5150=	NM_138712.5:c.-8-5150G>A

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#.

35 SubSNP, 14 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	PGA-UW-FHCRC	ss5587649	Oct 10, 2002 (108)
2	BCM_SSAHASNP	ss14206235	Dec 05, 2003 (119)
3	PARC	ss23143952	Sep 20, 2004 (126)
4	PGA-UW-FHCRC	ss28447572	Sep 21, 2004 (123)
5	PHARMGKB_PARC	ss69364853	May 16, 2007 (127)
6	PHARMGKB_PARC	ss69364856	May 16, 2007 (127)
7	ENSEMBL	ss161385253	Dec 01, 2009 (131)
8	1000GENOMES	ss330502331	May 09, 2011 (134)
9	TISHKOFF	ss556431069	Apr 25, 2013 (138)
10	EVA-GONL	ss978280169	Aug 21, 2014 (142)
11	JMKIDD_LAB	ss1070181166	Aug 21, 2014 (142)
12	1000GENOMES	ss1302834100	Aug 21, 2014 (142)
13	EVA_UK10K_ALSPAC	ss1606431382	Apr 01, 2015 (144)
14	EVA_UK10K_TWINSUK	ss1649425415	Apr 01, 2015 (144)
15	HAMMER_LAB	ss1798870862	Sep 08, 2015 (146)
16	WEILL_CORNELL_DGM	ss1921532754	Feb 12, 2016 (147)
17	JJLAB	ss2021319543	Sep 14, 2016 (149)
18	HUMAN_LONGEVITY	ss2249138476	Dec 20, 2016 (150)
19	GNOMAD	ss2789620004	Nov 08, 2017 (151)
20	EGCUT_WGS	ss3659742292	Jul 13, 2019 (153)
21	EVA_DECODE	ss3708652284	Jul 13, 2019 (153)
22	KHV_HUMAN_GENOMES	ss3802820362	Jul 13, 2019 (153)
23	EVA	ss3827665758	Apr 25, 2020 (154)
24	SGDP_PRJ	ss3855243276	Apr 25, 2020 (154)
25	TOPMED	ss4554471060	Apr 27, 2021 (155)
26	TOMMO_GENOMICS	ss5157834138	Apr 27, 2021 (155)
27	1000G_HIGH_COVERAGE	ss5253075654	Oct 13, 2022 (156)
28	EVA	ss5337942285	Oct 13, 2022 (156)
29	HUGCELL_USP	ss5452573850	Oct 13, 2022 (156)
30	EVA	ss5506887490	Oct 13, 2022 (156)
31	1000G_HIGH_COVERAGE	ss5530921034	Oct 13, 2022 (156)
32	SANFORD_IMAGENETICS	ss5631557650	Oct 13, 2022 (156)
33	TOMMO_GENOMICS	ss5689112367	Oct 13, 2022 (156)
34	EVA	ss5867661246	Oct 13, 2022 (156)
35	EVA	ss5959817699	Oct 13, 2022 (156)
36	1000Genomes	NC_000003.11 - 12416053	Oct 11, 2018 (152)
37	1000Genomes_30x	NC_000003.12 - 12374554	Oct 13, 2022 (156)
38	The Avon Longitudinal Study of Parents and Children	NC_000003.11 - 12416053	Oct 11, 2018 (152)
39	Genetic variation in the Estonian population	NC_000003.11 - 12416053	Oct 11, 2018 (152)
40	gnomAD - Genomes	NC_000003.12 - 12374554	Apr 27, 2021 (155)
41	Genome of the Netherlands Release 5	NC_000003.11 - 12416053	Apr 25, 2020 (154)
42	PharmGKB Aggregated	NC_000003.12 - 12374554	Apr 25, 2020 (154)
43	Qatari	NC_000003.11 - 12416053	Apr 25, 2020 (154)
44	SGDP_PRJ	NC_000003.11 - 12416053	Apr 25, 2020 (154)
45	8.3KJPN	NC_000003.11 - 12416053	Apr 27, 2021 (155)
46	14KJPN	NC_000003.12 - 12374554	Oct 13, 2022 (156)
47	TopMed	NC_000003.12 - 12374554	Apr 27, 2021 (155)
48	UK 10K study - Twins	NC_000003.11 - 12416053	Oct 11, 2018 (152)
49	ALFA	NC_000003.12 - 12374554	Apr 27, 2021 (155)

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)
rs12721156	Mar 10, 2006 (126)
rs17241188	Mar 10, 2006 (126)
rs17838663	Oct 07, 2004 (123)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
13980088, 7750082, 5480540, 3402705, 3574684, 7260256, 15803445, 7750082, ss330502331, ss556431069, ss978280169, ss1070181166, ss1302834100, ss1606431382, ss1649425415, ss1798870862, ss1921532754, ss2021319543, ss2789620004, ss3659742292, ss3827665758, ss3855243276, ss5157834138, ss5337942285, ss5506887490, ss5631557650, ss5959817699	NC_000003.11:12416052:G:A	NC_000003.12:12374553:G:A	(self)
18446969, 99256742, 7929, 22949471, 391848615, 15832457292, ss2249138476, ss3708652284, ss3802820362, ss4554471060, ss5253075654, ss5452573850, ss5530921034, ss5689112367, ss5867661246	NC_000003.12:12374553:G:A	NC_000003.12:12374553:G:A	(self)
ss14206235	NT_022517.16:12356052:G:A	NC_000003.12:12374553:G:A	(self)
ss5587649, ss23143952, ss28447572, ss69364853, ss69364856, ss161385253	NT_022517.18:12356052:G:A	NC_000003.12:12374553:G:A	(self)

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

No publications for rs4135318

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs4135318