PigVar

1.Mapping Information

Human SNP ID	rs17279437
Human chromosome	chr3
Human SNP position	45772602
Pig chromosome	chr13
Pig SNP position	32018974

2.Annotation Information

PubMed ID	21572414
Journal	Nat Genet
Link	www.ncbi.nlm.nih.gov/pubmed/21572414
Study	A genome-wide association study of metabolic traits in human urine.
Disease/Trait	Urinary metabolites
Initial sample	862 European ancestry male individuals
Replication sample	1,862 European ancestry individuals
Region	3p21.31
Chromosome id	chr3
Chromosome position	45772602
Reported gene	SLC6A20
Mapped gene	SLC6A20
Upstream gene id
Downstream gene id
SNP gene ids	54716
Upstream gene distance
Downstream gene distance
SNP risk allele	rs17279437-A
SNPs	rs17279437
Merged	0
SNP id current	17279437
Context	missense_variant
Intergenic	0
Allele frequency	0.115
P value	3E-19
Pvalue mlog	18.5228787452803
P value text	(Alanine/N,N-dimethylglycine ratio)
Or beta
%95 Ci
Platform	Affymetrix [645249]
CNV	N
Mapped trait	metabolite measurement
Mapped trait URI	http://www.ebi.ac.uk/efo/EFO_0004725
Study accession	GCST001073

PubMed ID	24816252
Journal	Nat Genet
Link	www.ncbi.nlm.nih.gov/pubmed/24816252
Study	An atlas of genetic influences on human blood metabolites.
Disease/Trait	Blood metabolite ratios
Initial sample	Up to 5,591 European ancestry individuals
Replication sample	Up to 1,767 European ancestry individuals
Region	3p21.31
Chromosome id	chr3
Chromosome position	45772602
Reported gene	SLC6A20
Mapped gene	SLC6A20
Upstream gene id
Downstream gene id
SNP gene ids	54716
Upstream gene distance
Downstream gene distance
SNP risk allele	rs17279437-A
SNPs	rs17279437
Merged	0
SNP id current	17279437
Context	missense_variant
Intergenic	0
Allele frequency	0.1
P value	2E-35
Pvalue mlog	34.698970004336
P value text	(X-11315/pyroglutamine)
Or beta	0.094
%95 Ci	[0.078-0.11] unit decrease
Platform	Affymetrix, Illumina [2100000] (imputed)
CNV	N
Mapped trait	blood metabolite measurement
Mapped trait URI	http://www.ebi.ac.uk/efo/EFO_0005664
Study accession	GCST002442

PubMed ID	24816252
Journal	Nat Genet
Link	www.ncbi.nlm.nih.gov/pubmed/24816252
Study	An atlas of genetic influences on human blood metabolites.
Disease/Trait	Blood metabolite levels
Initial sample	7,824 European ancestry individuals
Replication sample	NA
Region	3p21.31
Chromosome id	chr3
Chromosome position	45772602
Reported gene	SLC6A20
Mapped gene	SLC6A20
Upstream gene id
Downstream gene id
SNP gene ids	54716
Upstream gene distance
Downstream gene distance
SNP risk allele	rs17279437-A
SNPs	rs17279437
Merged	0
SNP id current	17279437
Context	missense_variant
Intergenic	0
Allele frequency	0.1
P value	1E-20
Pvalue mlog	20
P value text	(pyroglutamine)
Or beta	0.059
%95 Ci	[0.047-0.071] unit increase
Platform	Affymetrix, Illumina [2100000] (imputed)
CNV	N
Mapped trait	blood metabolite measurement
Mapped trait URI	http://www.ebi.ac.uk/efo/EFO_0005664
Study accession	GCST002443

PubMed ID	26352407
Journal	PLoS Genet
Link	www.ncbi.nlm.nih.gov/pubmed/26352407
Study	Genome-Wide Association Study with Targeted and Non-targeted NMR Metabolomics Identifies 15 Novel Loci of Urinary Human Metabolic Individuality.
Disease/Trait	Urinary metabolites
Initial sample	3,861 European ancestry individuals
Replication sample	1,691European ancestry individuals
Region	3p21.31
Chromosome id	chr3
Chromosome position	45772602
Reported gene	SLC6A20
Mapped gene	SLC6A20
Upstream gene id
Downstream gene id
SNP gene ids	54716
Upstream gene distance
Downstream gene distance
SNP risk allele	rs17279437-A
SNPs	rs17279437
Merged	0
SNP id current	17279437
Context	missense_variant
Intergenic	0
Allele frequency	0.11
P value	8E-60
Pvalue mlog	59.096910013008
P value text	(N,N-dimethylglycine/alanine)
Or beta	0.2827
%95 Ci	[NR] unit decrease
Platform	Affymetrix [620456]
CNV	N
Mapped trait	urinary metabolite measurement
Mapped trait URI	http://www.ebi.ac.uk/efo/EFO_0005116
Study accession	GCST003119

PubMed ID	26352407
Journal	PLoS Genet
Link	www.ncbi.nlm.nih.gov/pubmed/26352407
Study	Genome-Wide Association Study with Targeted and Non-targeted NMR Metabolomics Identifies 15 Novel Loci of Urinary Human Metabolic Individuality.
Disease/Trait	Urinary metabolites
Initial sample	3,861 European ancestry individuals
Replication sample	1,691European ancestry individuals
Region	3p21.31
Chromosome id	chr3
Chromosome position	45772602
Reported gene	SLC6A20
Mapped gene	SLC6A20
Upstream gene id
Downstream gene id
SNP gene ids	54716
Upstream gene distance
Downstream gene distance
SNP risk allele	rs17279437-A
SNPs	rs17279437
Merged	0
SNP id current	17279437
Context	missense_variant
Intergenic	0
Allele frequency	0.11
P value	8E-22
Pvalue mlog	21.096910013008
P value text	(2.916 ppm)
Or beta	0.2039
%95 Ci	[NR] unit decrease
Platform	Affymetrix [620456]
CNV	N
Mapped trait	urinary metabolite measurement
Mapped trait URI	http://www.ebi.ac.uk/efo/EFO_0005116
Study accession	GCST003119

THE PIG VARIATIONS AND POSITIVE SELECTION DATABASE