SNP Report

Basic Info

Name	rs7250872 dbSNP Ensembl
Location	chr19:1811604 - 1811604(1)
Variant Alleles	C/T
Minor Allele	T
Minor Allele Frequence	0.396166
Functional Annotation	5_prime_UTR_variant; downstream_gene_variant; missense_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant. Polyphen Annotation: benign(ENST00000310127, ENST00000587160); probably damaging(ENST00000531925) SIFT Annotation: deleterious - low confidence(ENST00000531925); tolerated - low confidence(ENST00000310127, ENST00000587160)
Consequence to Transcript	5_prime_UTR_variant(ENST00000525591, ENST00000526092); downstream_gene_variant(ENST00000170168, ENST00000411312, ENST00000586291, ENST00000587404, ENST00000590936); missense_variant(ENST00000310127, ENST00000587160, ENST00000531925); NMD_transcript_variant(ENST00000531925); non_coding_transcript_exon_variant(ENST00000533993); non_coding_transcript_variant(ENST00000533993); upstream_gene_variant(ENST00000586259)
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
Scott, L. J.,2009	T/C		NIMH/Pritzker: OR (95% CI)=1.18(1.01-1.37), P-value = 0.035;...... NIMH/Pritzker: OR (95% CI)=1.18(1.01-1.37), P-value = 0.035; GSK(reduced sample): OR (95% CI)=1.33(1.14-1.56), P-value = 0.00043; WTCCC: OR (95% CI)=1.18(1.06-1.30), P-value = 0.0024; 3-study meta-analysis: OR (95% CI)=1.21(1.12-1.31), P-value = 0.0000017; Heterogeneity: I²%=0, P-value = 0.41 More...		Trend

SNP related genes (count: 2)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
ATP8B3	ATPase, aminophospholipid transporter, class I, type 8B, member 3	19p13.3	Mapped by Literature SNP
REXO1	REX1, RNA exonuclease 1 homolog (S. cerevisiae)	19p13.3	Mapped by Literature SNP

SNPs in LD with rs7250872 (count: 3) View in gBrowse (chr19:1809599..1812522 )

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]
rs7260237	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.833[CEU]
rs10421558	downstream_gene_variant; upstream_gene_variant	0.876[CEU]
rs9941464	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.833[CEU]

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

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