PigVar

1.Mapping Information

Human SNP ID	rs17145738
Human chromosome	chr7
Human SNP position	73568544
Pig chromosome	chr3
Pig SNP position	10584802

2.Annotation Information

PubMed ID	18193044
Journal	Nat Genet
Link	www.ncbi.nlm.nih.gov/pubmed/18193044
Study	Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans.
Disease/Trait	Triglycerides
Initial sample	2,758 individuals
Replication sample	18,544 individuals
Region	7q11.23
Chromosome id	chr7
Chromosome position	73568544
Reported gene	TBL2, MLXIPL, BCL7B
Mapped gene	BCL7B - TBL2
Upstream gene id	9275
Downstream gene id	26608
SNP gene ids
Upstream gene distance	10809
Downstream gene distance	400
SNP risk allele	rs17145738-T
SNPs	rs17145738
Merged	0
SNP id current	17145738
Context	downstream_gene_variant
Intergenic	1
Allele frequency	0.13
P value	7E-22
Pvalue mlog	21.1549019599857
P value text
Or beta	0.14
%95 Ci	[0.25-0.53] percentage SD decrease
Platform	Affymetrix [389878]
CNV	N
Mapped trait	triglyceride measurement
Mapped trait URI	http://www.ebi.ac.uk/efo/EFO_0004530
Study accession	GCST000138

PubMed ID	18193043
Journal	Nat Genet
Link	www.ncbi.nlm.nih.gov/pubmed/18193043
Study	Newly identified loci that influence lipid concentrations and risk of coronary artery disease.
Disease/Trait	Triglycerides
Initial sample	8,684 European ancestry individuals
Replication sample	9,741 European ancestry individuals
Region	7q11.23
Chromosome id	chr7
Chromosome position	73568544
Reported gene	MLXIPL
Mapped gene	BCL7B - TBL2
Upstream gene id	9275
Downstream gene id	26608
SNP gene ids
Upstream gene distance	10809
Downstream gene distance	400
SNP risk allele	rs17145738-C
SNPs	rs17145738
Merged	0
SNP id current	17145738
Context	downstream_gene_variant
Intergenic	1
Allele frequency	0.84
P value	0.000000000002
Pvalue mlog	11.698970004336
P value text
Or beta	8.21
%95 Ci	[NR] mg/dl increase
Platform	Affymetrix, Illumina [~ 2261000] (imputed)
CNV	N
Mapped trait	triglyceride measurement
Mapped trait URI	http://www.ebi.ac.uk/efo/EFO_0004530
Study accession	GCST000139

PubMed ID	20686565
Journal	Nature
Link	www.ncbi.nlm.nih.gov/pubmed/20686565
Study	Biological, clinical and population relevance of 95 loci for blood lipids.
Disease/Trait	HDL cholesterol
Initial sample	99,900 European ancestry individuals
Replication sample	NA
Region	7q11.23
Chromosome id	chr7
Chromosome position	73568544
Reported gene	MLXIPL
Mapped gene	BCL7B - TBL2
Upstream gene id	9275
Downstream gene id	26608
SNP gene ids
Upstream gene distance	10809
Downstream gene distance	400
SNP risk allele	rs17145738-T
SNPs	rs17145738
Merged	0
SNP id current	17145738
Context	downstream_gene_variant
Intergenic	1
Allele frequency	0.12
P value	0.000000001
Pvalue mlog	9
P value text
Or beta	0.57
%95 Ci	[0.33-0.81] mg/dL increase
Platform	Affymetrix, Illumina, Perlegen [~ 2600000] (imputed)
CNV	N
Mapped trait	high density lipoprotein cholesterol measurement
Mapped trait URI	http://www.ebi.ac.uk/efo/EFO_0004612
Study accession	GCST000755

PubMed ID	20686565
Journal	Nature
Link	www.ncbi.nlm.nih.gov/pubmed/20686565
Study	Biological, clinical and population relevance of 95 loci for blood lipids.
Disease/Trait	Triglycerides
Initial sample	96,598 European ancestry individuals
Replication sample	NA
Region	7q11.23
Chromosome id	chr7
Chromosome position	73568544
Reported gene	MLXIPL
Mapped gene	BCL7B - TBL2
Upstream gene id	9275
Downstream gene id	26608
SNP gene ids
Upstream gene distance	10809
Downstream gene distance	400
SNP risk allele	rs17145738-G
SNPs	rs17145738
Merged	0
SNP id current	17145738
Context	downstream_gene_variant
Intergenic	1
Allele frequency	0.19
P value	9E-59
Pvalue mlog	58.0457574905606
P value text
Or beta	7.91
%95 Ci	[6.93-8.89] mg/dL decrease
Platform	Affymetrix, Illumina, Perlegen [~ 2600000] (imputed)
CNV	N
Mapped trait	triglyceride measurement
Mapped trait URI	http://www.ebi.ac.uk/efo/EFO_0004530
Study accession	GCST000758

PubMed ID	24097068
Journal	Nat Genet
Link	www.ncbi.nlm.nih.gov/pubmed/24097068
Study	Discovery and refinement of loci associated with lipid levels.
Disease/Trait	HDL cholesterol
Initial sample	94,595 European ancestry individuals
Replication sample	93,982 European ancestry individuals
Region	7q11.23
Chromosome id	chr7
Chromosome position	73568544
Reported gene	MLXIPL
Mapped gene	BCL7B - TBL2
Upstream gene id	9275
Downstream gene id	26608
SNP gene ids
Upstream gene distance	10809
Downstream gene distance	400
SNP risk allele	rs17145738-T
SNPs	rs17145738
Merged	0
SNP id current	17145738
Context	downstream_gene_variant
Intergenic	1
Allele frequency	0.13
P value	0.0000000000005
Pvalue mlog	12.3010299956639
P value text
Or beta	0.041
%95 Ci	[NR] unit increase
Platform	NR [NR] (imputed)
CNV	N
Mapped trait	high density lipoprotein cholesterol measurement
Mapped trait URI	http://www.ebi.ac.uk/efo/EFO_0004612
Study accession	GCST002223

PubMed ID	24097068
Journal	Nat Genet
Link	www.ncbi.nlm.nih.gov/pubmed/24097068
Study	Discovery and refinement of loci associated with lipid levels.
Disease/Trait	Triglycerides
Initial sample	94,595 European ancestry individuals
Replication sample	93,982 European ancestry individuals
Region	7q11.23
Chromosome id	chr7
Chromosome position	73568544
Reported gene	MLXIPL
Mapped gene	BCL7B - TBL2
Upstream gene id	9275
Downstream gene id	26608
SNP gene ids
Upstream gene distance	10809
Downstream gene distance	400
SNP risk allele	rs17145738-T
SNPs	rs17145738
Merged	0
SNP id current	17145738
Context	downstream_gene_variant
Intergenic	1
Allele frequency	0.13
P value	9E-99
Pvalue mlog	98.0457574905606
P value text
Or beta	0.115
%95 Ci	[NR] mg/dL decrease
Platform	NR [NR] (imputed)
CNV	N
Mapped trait	triglyceride measurement
Mapped trait URI	http://www.ebi.ac.uk/efo/EFO_0004530
Study accession	GCST002216

THE PIG VARIATIONS AND POSITIVE SELECTION DATABASE