SNP Report

Basic Info

Name	rs1390938 dbSNP Ensembl
Location	chr8:20179202 - 20179202(1)
Variant Alleles	A/G
Ancestral Allele	T
Minor Allele	A
Minor Allele Frequence	0.255791
Functional Annotation	missense_variant; NMD_transcript_variant; upstream_gene_variant. Polyphen Annotation: benign(ENST00000265808, ENST00000276373, ENST00000381608, ENST00000437980, ENST00000440926, ENST00000517776, ENST00000519026, ENST00000522513) SIFT Annotation: tolerated(ENST00000265808, ENST00000276373, ENST00000381608, ENST00000437980, ENST00000440926, ENST00000517776, ENST00000519026, ENST00000522513)
Consequence to Transcript	missense_variant(ENST00000265808, ENST00000276373, ENST00000381608, ENST00000437980, ENST00000440926, ENST00000517776, ENST00000519026, ENST00000522513); NMD_transcript_variant(ENST00000517776); upstream_gene_variant(ENST00000524272)
No. of Studies	2 (Positive: 1; Negative: 1; Trend: 0)
Source	Literature
Overlap with SZ?	NO
Overlap with MDD?	NO

SNP related studies (count: 2)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Lohoff, F. W., 2006	Thr/Ile		genotypic P-value = 0.009, allelic P-value = 0.003 for BPI ;...... genotypic P-value = 0.009, allelic P-value = 0.003 for BPI ; genotypic P-value = 0.063, allelic P-value = 0.02 for BP I psychosis More...	The potential functional polymorphism Thr136Ile in VMAT1 was...... The potential functional polymorphism Thr136Ile in VMAT1 was associated with BPD More...	Positive
Yosifova, A.,2009	A/G		Allelic association: P-value = 0.38 Allelic association: P-value = 0.38	No significant association was observed No significant association was observed	Negative

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
SLC18A1	solute carrier family 18 (vesicular monoamine transporter), member 1	8p21.3	3(2/1/0)

SNPs in LD with rs1390938 (count: 7) View in gBrowse (chr8:20171753..20182160 )

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]
rs2132699	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CEU]; 0.906[TSI]
rs4921694	intron_variant; NMD_transcript_variant; upstream_gene_variant	1.0[CEU]
rs6992927	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CEU]; 0.937[TSI]
rs952859	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CEU]; 0.968[TSI]
rs7006986	intron_variant; NMD_transcript_variant; upstream_gene_variant	1.0[CEU]
rs952858	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CEU]
rs6586898	intron_variant; NMD_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)