SNP Report

Basic Info

Name	rs2289700 dbSNP Ensembl
Location	chr15:78932341 - 78932341(1)
Variant Alleles	C/T
Ancestral Allele	T
Minor Allele	T
Minor Allele Frequence	0.306709
Functional Annotation	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant.
Consequence to Transcript	downstream_gene_variant(ENST00000530010, ENST00000530929, ENST00000534268); intron_variant(ENST00000220166, ENST00000525807, ENST00000528191, ENST00000528741, ENST00000529263, ENST00000529612, ENST00000529861, ENST00000533777, ENST00000534038, ENST00000534533, ENST00000615999); NMD_transcript_variant(ENST00000525807, ENST00000529861, ENST00000533777); non_coding_transcript_variant(ENST00000528191, ENST00000529263, ENST00000529612, ENST00000534038, ENST00000534533); upstream_gene_variant(ENST00000527138, ENST00000534237)
No. of Studies	1 (Positive: 0; Negative: 0; Trend: 1)
Source	Literature
Overlap with SZ?	NO
Overlap with MDD?	NO

SNP related studies (count: 1)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Yosifova, A.,2011	G>A		GWAS P-value = 0.0000026, OR(95%CI)=2.7(1.74-4.19); Replicat...... GWAS P-value = 0.0000026, OR(95%CI)=2.7(1.74-4.19); Replication P-value = 0.171, OR(95%CI)=1.47(0.88-2.45); Mantel-Haenszel P-value = 0.00000914, OR(95%CI)=2.13(1.53-2.95) More...	Suggestive association was found. Suggestive association was found.	Trend

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
CTSH	cathepsin H	15q25.1	1(0/0/1)

SNPs in LD with rs2289700 (count: 3) View in gBrowse (chr15:78925289..78936029 )

The LD data used here is based on HapMap rel#27. LD SNP pairs were selected with a threshold r²<=0.8.

rs_ID	Functional Annotation	r²[population]
rs8034542	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CEU]
rs2289695	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CEU]
rs2289697	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CEU]; 1.0[TSI]

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

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