PigVar

1.Mapping Information

Human SNP ID	rs1346
Human chromosome	chr11
Human SNP position	65569780
Pig chromosome	chr2
Pig SNP position	5908048

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	11q13.1
Chromosome id	chr11
Chromosome position	65569780
Reported gene	SSSCA1
Mapped gene	SSSCA1-AS1
Upstream gene id
Downstream gene id
SNP gene ids	254100
Upstream gene distance
Downstream gene distance
SNP risk allele	rs1346-T
SNPs	rs1346
Merged	0
SNP id current	1346
Context	non_coding_transcript_exon_variant
Intergenic	0
Allele frequency	NR
P value	0.0000000000005
Pvalue mlog	12.3010299956639
P value text
Or beta	0.012
%95 Ci	[0.0081-0.0159] unit decrease
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	11q13.1
Chromosome id	chr11
Chromosome position	65569780
Reported gene	SSSCA1
Mapped gene	SSSCA1-AS1
Upstream gene id
Downstream gene id
SNP gene ids	254100
Upstream gene distance
Downstream gene distance
SNP risk allele	rs1346-T
SNPs	rs1346
Merged	0
SNP id current	1346
Context	non_coding_transcript_exon_variant
Intergenic	0
Allele frequency	0.19
P value	0.000000002
Pvalue mlog	8.69897000433601
P value text
Or beta	0.019
%95 Ci	[0.013-0.025] unit decrease
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	11q13.1
Chromosome id	chr11
Chromosome position	65569780
Reported gene	SSSCA1
Mapped gene	SSSCA1-AS1
Upstream gene id
Downstream gene id
SNP gene ids	254100
Upstream gene distance
Downstream gene distance
SNP risk allele	rs1346-T
SNPs	rs1346
Merged	0
SNP id current	1346
Context	non_coding_transcript_exon_variant
Intergenic	0
Allele frequency	0.19
P value	0.00000000007
Pvalue mlog	10.1549019599857
P value text	(EA)
Or beta	0.023
%95 Ci	[0.015-0.031] unit decrease
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