PigVar

1.Mapping Information

Human SNP ID	rs2623325
Human chromosome	chr3
Human SNP position	99412911
Pig chromosome	chr13
Pig SNP position	169747493

2.Annotation Information

PubMed ID	25241763
Journal	Nat Commun
Link	www.ncbi.nlm.nih.gov/pubmed/25241763
Study	Meta-analysis of genome-wide association studies identifies novel loci that influence cupping and the glaucomatous process.
Disease/Trait	Vertical cup-disc ratio
Initial sample	18,963 European ancestry individuals, 2,131 Erasmus Rucphen individuals
Replication sample	2,453 Chinese ancestry individuals, 2,026 Indian ancestry individuals, 2,305 Malay ancestry individuals
Region	3q12.1
Chromosome id	chr3
Chromosome position	99412911
Reported gene	COL8A1
Mapped gene	LOC105374004 - LOC105374005
Upstream gene id	105374004
Downstream gene id	105374005
SNP gene ids
Upstream gene distance	75256
Downstream gene distance	88847
SNP risk allele	rs2623325-A
SNPs	rs2623325
Merged	0
SNP id current	2623325
Context	intergenic_variant
Intergenic	1
Allele frequency	NR
P value	0.0000000007
Pvalue mlog	9.15490195998574
P value text
Or beta	0.016
%95 Ci	[0.010-0.022] unit increase
Platform	Affymetrix, Illumina [~ 2500000] (imputed)
CNV	N
Mapped trait	optic disc size measurement
Mapped trait URI	http://www.ebi.ac.uk/efo/EFO_0004832
Study accession	GCST002626

PubMed ID	25631615
Journal	Genet Epidemiol
Link	www.ncbi.nlm.nih.gov/pubmed/25631615
Study	Meta-analysis of Genome-Wide Association Studies Identifies Novel Loci Associated With Optic Disc Morphology.
Disease/Trait	Optic cup area
Initial sample	15,087 European ancestry individuals, 2,131 Erasmus Rucphen Family individuals
Replication sample	2,363 Chinese ancestry individuals, 2,225 Malay ancestry individuals, 2,025 Indian ancestry individuals
Region	3q12.1
Chromosome id	chr3
Chromosome position	99412911
Reported gene	COL8A1
Mapped gene	LOC105374004 - LOC105374005
Upstream gene id	105374004
Downstream gene id	105374005
SNP gene ids
Upstream gene distance	75256
Downstream gene distance	88847
SNP risk allele	rs2623325-A
SNPs	rs2623325
Merged	0
SNP id current	2623325
Context	intergenic_variant
Intergenic	1
Allele frequency	0.11
P value	0.00000004
Pvalue mlog	7.39794000867203
P value text
Or beta	0.025
%95 Ci	[0.015-0.035] unit increase
Platform	Affymetrix, Illumina [~ 2500000] (imputed)
CNV	N
Mapped trait	optic cup area measurement
Mapped trait URI	http://www.ebi.ac.uk/efo/EFO_0006940
Study accession	GCST002762

PubMed ID	25631615
Journal	Genet Epidemiol
Link	www.ncbi.nlm.nih.gov/pubmed/25631615
Study	Meta-analysis of Genome-Wide Association Studies Identifies Novel Loci Associated With Optic Disc Morphology.
Disease/Trait	Optic cup area
Initial sample	15,087 European ancestry individuals, 2,131 Erasmus Rucphen Family individuals
Replication sample	2,363 Chinese ancestry individuals, 2,225 Malay ancestry individuals, 2,025 Indian ancestry individuals
Region	3q12.1
Chromosome id	chr3
Chromosome position	99412911
Reported gene	COL8A1
Mapped gene	LOC105374004 - LOC105374005
Upstream gene id	105374004
Downstream gene id	105374005
SNP gene ids
Upstream gene distance	75256
Downstream gene distance	88847
SNP risk allele	rs2623325-A
SNPs	rs2623325
Merged	0
SNP id current	2623325
Context	intergenic_variant
Intergenic	1
Allele frequency	0.11
P value	0.00000002
Pvalue mlog	7.69897000433601
P value text	(EA)
Or beta	0.039
%95 Ci	[0.025-0.053] unit increase
Platform	Affymetrix, Illumina [~ 2500000] (imputed)
CNV	N
Mapped trait	optic cup area measurement
Mapped trait URI	http://www.ebi.ac.uk/efo/EFO_0006940
Study accession	GCST002762

THE PIG VARIATIONS AND POSITIVE SELECTION DATABASE