SNP Report

Basic Info

Name	rs1024582 dbSNP Ensembl
Location	chr12:2293080 - 2293080(1)
Variant Alleles	A/G
Ancestral Allele	G
Minor Allele	A
Minor Allele Frequence	0.168131
Functional Annotation	downstream_gene_variant; intron_variant.
Consequence to Transcript	downstream_gene_variant(ENST00000542680); intron_variant(ENST00000327702, ENST00000335762, ENST00000344100, ENST00000347598, ENST00000399591, ENST00000399595, ENST00000399597, ENST00000399601, ENST00000399603, ENST00000399606, ENST00000399617, ENST00000399621, ENST00000399629, ENST00000399634, ENST00000399637, ENST00000399638, ENST00000399641, ENST00000399644, ENST00000399649, ENST00000399655, ENST00000402845, ENST00000406454, ENST00000480911, LRG_334t1, LRG_334t2, LRG_334t3, LRG_334t4)
No. of Studies	2 (Positive: 2; Negative: 0; Trend: 0)
Source	Literature
Overlap with SZ?	YES
Overlap with MDD?	YES

SNP related studies (count: 2)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Cross-Disorder Group of the Psychiatric Genomics Consortium,2013	A/G		Association analysis:P-value = 0.0000000187,OR(95%CI) = 1.07...... Association analysis:P-value = 0.0000000187,OR(95%CI) = 1.07(1.05-1.10) when BD and SZ were combined More...	Significant association was observed in cross-disorder analy...... Significant association was observed in cross-disorder analysis. More...	Positive
Ferreira, M. A.,2008		A	Imputed P value=1.7E-08, OR=1.18 in the combined analysis of...... Imputed P value=1.7E-08, OR=1.18 in the combined analysis of WTCCC, STEP-UCL and ED-DUB-STEP2 datasets. Imputed P value=0.0019 in the WTCCC. Imputed P value=0.0012 in the STEP-UCL. Imputed P value=0.0056 in the ED-DUB-STEP2 dataset. More...		Positive

SNP related genes (count: 2)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
CACNA1C	calcium channel, voltage-dependent, L type, alpha 1C subunit	12p13.3	20(17/3/0)
CACNA1C-IT3	CACNA1C intronic transcript 3	12p13.33	Mapped by Literature SNP

SNPs in LD with rs1024582 (count: 6) View in gBrowse (chr12:2237664..2299028 )

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]
rs12315711	intron_variant	0.92[CEU]
rs4298967	intron_variant	1.0[CEU]; 1.0[TSI]
rs10774036	intron_variant; non_coding_transcript_variant	0.959[CEU]
rs10774035	intron_variant	0.92[CEU]; 0.91[TSI]
rs11062170	intron_variant	0.92[CEU]
rs10744560	intron_variant; non_coding_transcript_variant	0.959[CEU]; 0.969[TSI]

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

Reference	Statistical Result	Description	Result Category
Cross-Disorder Group of the Psychiatric Genomics Consortium,2013	Association analysis:P-value = 0.0000000187,OR(95%CI) = 1.07(1.05-1.10) when BD and SZ were combined	Significant association was observed in cross-disorder analysis.	Positive

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

Reference	Statistical Result	Description	Result Category
Cross-Disorder Group of the Psychiatric Genomics Consortium,2013	Association analysis:P-value = 0.0000000187,OR(95%CI) = 1.07(1.05-1.10) when BD and SZ were combined	Significant association was observed in cross-disorder analysis.	Positive