SNP Report

Basic Info

Name	rs2284178 dbSNP Ensembl
Location	chrCHR_HSCHR6_MHC_SSTO_CTG1:31455062 - 31455062(1)
Variant Alleles	C/T
Ancestral Allele	C
Minor Allele	T
Minor Allele Frequence	0.46905
Functional Annotation	downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant.
Consequence to Transcript	downstream_gene_variant(ENST00000460889); intron_variant(ENST00000467369); non_coding_transcript_exon_variant(ENST00000414046, ENST00000541196); non_coding_transcript_variant(ENST00000414046, ENST00000467369, ENST00000541196); upstream_gene_variant(ENST00000440087, ENST00000419355, ENST00000438873, ENST00000419355, ENST00000438873, ENST00000455463, ENST00000457127, ENST00000455463, ENST00000457127, ENST00000447631, ENST00000423496, ENST00000423496)
No. of Studies	1 (Positive: 1; Negative: 0; Trend: 0)
Source	Literature
Overlap with SZ?	YES
Overlap with MDD?	NO

SNP related studies (count: 1)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Andreassen OA, 2013			Conditional FDR; SCZ loci given BD: FDR=0.036 for SCZ and BD Conditional FDR; SCZ loci given BD: FDR=0.036 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
HCP5	HLA complex P5 (non-protein coding)	6p21.3	Mapped by Literature SNP

SNPs in LD with rs2284178 (count: 0) View in gBrowse (chrCHR_HSCHR6_MHC_SSTO_CTG1:31455062..31455062 )

Overlap with SZ from cross-disorder studies (count: 1)

Reference	Statistical Result	Description	Result Category
Andreassen OA, 2013	Conditional FDR; SCZ loci given BD: P-value=0.000331, FDR=0.316, FDR=0.036 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32.	Positive

Overlap with MDD from cross-disorder studies (count: 0)