SNP Report

Basic Info

Name	rs1012053 dbSNP Ensembl
Location	chr13:42079301 - 42079301(1)
Variant Alleles	C/A
Ancestral Allele	A
Minor Allele	C
Minor Allele Frequence	0.229233
Functional Annotation	intron_variant.
Consequence to Transcript	intron_variant(ENST00000261491, ENST00000337343, ENST00000379274)
No. of Studies	6 (Positive: 1; Negative: 5; Trend: 0)
Source	Literature
Overlap with SZ?	YES
Overlap with MDD?	YES

SNP related studies (count: 6)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Baum, A. E., 2008 (b)		A	Random effects P-value = 0.044; DerSimonian-Laird (random e...... Random effects P-value = 0.044; DerSimonian-Laird (random effects) OR (95% CI)=1.38 (1.01, 1.89) More...		Negative
Yosifova, A.,2009	A/C		Allelic association: P-value = 0.74 Allelic association: P-value = 0.74	No significant association was observed No significant association was observed	Negative
Takata, A.,2011(a)	A/C		Fisher's exact test: allele P-value = 0.9169, genotype P-val...... Fisher's exact test: allele P-value = 0.9169, genotype P-value = 0.8578 More...	No significant association was observed in BD. No significant association was observed in BD.	Negative
Squassina, A.,2009		A	Alelle association: P-value = 0.881permutation P-value = 1 Alelle association: P-value = 0.881permutation P-value = 1	No significant association was observed No significant association was observed	Negative
Zeng, Z.,2011		A	Allelic association: P-value = 0.191, permutated P-value = 0...... Allelic association: P-value = 0.191, permutated P-value = 0.829 for BPD; P-value = 0.15, permutated P-value = 0.739 for BPDI More...	No significant association was observed in BD. No significant association was observed in BD.	Negative
Baum, A. E., 2008 (a)		A	P-value = 0.0002 when genotyped individually in the test sam...... P-value = 0.0002 when genotyped individually in the test sample (NIMH); P-value = 1.5E-05 when individually genotyped in the Replication sample (German); P-value = 1.5E-08 in the combined dataset. OR (95% CI)=1.59 (1.35-1.87) More...	significant at the P < 0.05 level in both samples. This SNP ...... significant at the P < 0.05 level in both samples. This SNP is significant at the experiment-wide P < 0.01 after Bonferroni correction of the combined results for the total number of SNPs studied. More...	Positive

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
DGKH	diacylglycerol kinase, eta	13q13.3	6(3/3/0)

SNPs in LD with rs1012053 (count: 13) View in gBrowse (chr13:42069058..42127805 )

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: 13)

rs_ID	Functional Annotation	r²[population]
rs7990452	intron_variant; upstream_gene_variant	0.868[CHB]; 0.824[JPT]
rs9532987	intron_variant; upstream_gene_variant	0.865[CHB]; 0.824[JPT]
rs1170158	intron_variant	0.813[TSI]
rs9532989	intron_variant; upstream_gene_variant	0.868[CHB]; 0.824[JPT]
rs9532985	downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	0.954[CHB]; 1.0[CHD]; 0.953[JPT]
rs9525566	downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	0.954[CHB]; 0.905[JPT]
rs1170187	intron_variant	0.813[TSI]
rs2253650	intron_variant	1.0[CEU]; 1.0[TSI]; 1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs1170188	intron_variant	0.813[TSI]; 0.814[CHD]
rs1177637	intron_variant	0.813[TSI]
rs4142112	intron_variant; upstream_gene_variant	0.868[CHB]; 0.82[JPT]
rs669642	intron_variant	1.0[CEU]; 1.0[CHB]; 1.0[JPT]
rs670676	intron_variant	0.812[TSI]

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

Reference	Statistical Result	Description	Result Category
Zeng, Z.,2011	Allelic association:P-value = 0.074, permutated P-value = 0.494 for SCZ	No significant association was observed after permutation.	Negative

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

Reference	Statistical Result	Description	Result Category
Zeng, Z.,2011	Allelic association:P-value > 0.05 for MDD.	No significant association was observed after permutation.	Negative