SNP Report

Basic Info

Name	rs472913 dbSNP Ensembl
Location	chr1:60629886 - 60629886(1)
Variant Alleles	G/C
Ancestral Allele	G
Minor Allele	G
Minor Allele Frequence	0.47484
Functional Annotation	intron_variant; non_coding_transcript_variant.
Consequence to Transcript	intron_variant(ENST00000439156); non_coding_transcript_variant(ENST00000439156)
No. of Studies	2 (Positive: 0; Negative: 1; Trend: 1)
Source	Literature
Overlap with SZ?	YES
Overlap with MDD?	NO

SNP related studies (count: 2)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Scott, L. J.,2009	C/G		NIMH/Pritzker: OR (95% CI)=1.12(0.97-1.29), P-value = 0.11; ...... NIMH/Pritzker: OR (95% CI)=1.12(0.97-1.29), P-value = 0.11; GSK(reduced sample): OR (95% CI)=1.17(1.00-1.36), P-value = 0.051; WTCCC: OR (95% CI)=1.20?(1.11-1.28), P-value = 0.00000063; 3-study meta-analysis: OR (95% CI)=1.18(1.11-1.25), P-value = 0.0000002; Heterogeneity: I²%=0, P-value = 0.72 More...		Trend
Kondo, K.,2013	G/C		P-value = 0.20,OR= 0.945 P-value = 0.20,OR= 0.945	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)
NFIX	nuclear factor I/X (CCAAT-binding transcription factor)	19p13.3	4(0/3/1)

SNPs in LD with rs472913 (count: 29) View in gBrowse (chr1:60594841..60659706 )

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

Literature-origin SNPs (count: 0)

LD-proxies (count: 29)

rs_ID	Functional Annotation	r²[population]
rs10218679	intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.844[CEU]
rs576932	intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[JPT]
rs580085	downstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs528037	intron_variant; non_coding_transcript_variant	1.0[CHB]; 0.911[JPT]
rs555988		1.0[CHB]; 1.0[JPT]
rs494011		0.927[CEU]; 1.0[CHB]; 1.0[JPT]
rs524439	intron_variant; non_coding_transcript_variant	1.0[CHB]; 0.913[JPT]
rs550049	downstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs564367		0.96[CEU]; 1.0[CHB]; 1.0[JPT]
rs483231		1.0[CHB]; 1.0[JPT]
rs548089	downstream_gene_variant	0.95[CHB]; 1.0[JPT]
rs814197	intron_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CEU]; 1.0[CHB]; 1.0[JPT]
rs496946	intron_variant; non_coding_transcript_variant	1.0[CHB]; 0.909[JPT]
rs1841565	intron_variant; non_coding_transcript_variant	0.963[CEU]; 0.95[CHB]; 0.913[JPT]
rs2989477	intron_variant; non_coding_transcript_variant	0.963[CEU]; 0.95[CHB]; 0.913[JPT]
rs569710		1.0[CHB]; 1.0[JPT]
rs2447043	intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[JPT]
rs489543	downstream_gene_variant	0.963[CEU]; 0.95[CHB]; 1.0[JPT]
rs473149	intron_variant; non_coding_transcript_variant	0.884[CHB]; 0.889[JPT]
rs528598	intron_variant; non_coding_transcript_variant	0.806[CEU]
rs473368	downstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs1335811	downstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs552294	intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.808[CEU]
rs2481979	downstream_gene_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	0.899[CHB]; 0.825[JPT]
rs497005		1.0[CHB]; 1.0[JPT]
rs555070	intron_variant; non_coding_transcript_variant	1.0[CHB]; 0.909[JPT]
rs514413	intron_variant; non_coding_transcript_variant	0.948[CHB]; 0.913[JPT]
rs484743	intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.844[CEU]
rs514512	intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[JPT]

Overlap with SZ from cross-disorder studies (count: 1)

Reference	Statistical Result	Description	Result Category
Kondo, K.,2013	P-value = 0.036,OR= 0.888	Significant association was observed.	Positive

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