SNP Report

Basic Info

Name	rs12540583 dbSNP Ensembl
Location	chrCHR_HSCHR7_1_CTG4_4:103211227 - 103211227(-1)
Variant Alleles	C/A
Ancestral Allele	A
Minor Allele	C
Minor Allele Frequence	0.167931
Functional Annotation	downstream_gene_variant; missense_variant; NMD_transcript_variant; upstream_gene_variant; intron_variant; non_coding_transcript_variant. Polyphen Annotation: benign(ENST00000341533, ENST00000417955, ENST00000422589, ENST00000427257, ENST00000465647) SIFT Annotation: tolerated(ENST00000341533, ENST00000417955, ENST00000422589, ENST00000427257, ENST00000465647)
Consequence to Transcript	downstream_gene_variant(ENST00000418294); missense_variant(ENST00000341533, ENST00000417955, ENST00000422589, ENST00000427257, ENST00000465647); NMD_transcript_variant(ENST00000422589); upstream_gene_variant(ENST00000414118, ENST00000420631); intron_variant(ENST00000631820, ENST00000631940, ENST00000632400, ENST00000632491, ENST00000633207); non_coding_transcript_variant(ENST00000631820, ENST00000631940, ENST00000632400, ENST00000632491, ENST00000633207)
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
Pisanu, C., 2013	C/A		logistic regression, P-value=0.7, OR=0.92 logistic regression, P-value=0.7, OR=0.92	Nominal association with BD or lithium response was not obse...... Nominal association with BD or lithium response was not observed in this study. More...	Negative

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
NAPEPLD	N-acyl phosphatidylethanolamine phospholipase D	7q22.1	1(1/0/0)

SNPs in LD with rs12540583 (count: 4) View in gBrowse (chrCHR_HSCHR7_1_CTG4_4:102934473..103316709 )

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]
rs1057066	downstream_gene_variant; intron_variant; missense_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.899[CEU]
rs3948710	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	1.0[CEU]
rs3757508	upstream_gene_variant	1.0[CEU]
rs12537821	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CEU]; 0.911[TSI]

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

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