SNP Report

Basic Info

Name	rs9817739 dbSNP Ensembl
Location	chr3:16439320 - 16439320(1)
Variant Alleles	G/A
Ancestral Allele	G
Minor Allele	A
Minor Allele Frequence	0.21865
Functional Annotation	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant.
Consequence to Transcript	intron_variant(ENST00000334133, ENST00000431547, ENST00000432519, ENST00000441460, ENST00000449415, ENST00000451036, ENST00000453536, ENST00000470458, ENST00000484752); NMD_transcript_variant(ENST00000453536); non_coding_transcript_variant(ENST00000470458, ENST00000484752); upstream_gene_variant(ENST00000495666)
No. of Studies	1 (Positive: 0; Negative: 1; Trend: 0)
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
Sklar, P., 2008	T/C		CMH (Cochran-Mantel-Haenszel) P-value = 3.47E-05, allelic P-...... CMH (Cochran-Mantel-Haenszel) P-value = 3.47E-05, allelic P-value = 7.26E-05, OR=0.79, pSNP test P-value = 7.30E-05, pHAP test P-value = 7.24E-03, r²=0.28 More...		Negative

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
RFTN1	raftlin, lipid raft linker 1	3p24.3	Mapped by Literature SNP

SNPs in LD with rs9817739 (count: 2) View in gBrowse (chr3:16437039..16439320 )

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

rs_ID	Literature-origin SNPs with LD	Functional Annotation	r²[population]
rs11715118		intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.831[CEU]; 0.926[TSI]
rs9839841		intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.831[CEU]

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

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