SNP Report

Basic Info

Name	rs228642 dbSNP Ensembl
Location	chr1:7803233 - 7803233(1)
Variant Alleles	C/T
Ancestral Allele	C
Minor Allele	T
Minor Allele Frequence	0.416334
Functional Annotation	intron_variant; non_coding_transcript_variant.
Consequence to Transcript	intron_variant(ENST00000361923, ENST00000377532, ENST00000377541, ENST00000463106, ENST00000613533, ENST00000614998); non_coding_transcript_variant(ENST00000463106)
No. of Studies	2 (Positive: 1; Negative: 1; Trend: 0)
Source	Literature
Overlap with SZ?	NO
Overlap with MDD?	YES

SNP related studies (count: 2)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Soria, V.,2010			X²-tests: allele P-value = 0.202, Model Recessive...... X²-tests: allele P-value = 0.202, Model Recessive, genotype P-value = 0.028, OR(95%CI)=1.66 (1.06-2.60) More...	Significant association was found in BD. Significant association was found in BD.	Positive
Yosifova, A.,2009	C/T		Allelic association: P-value = 0.52 Allelic association: P-value = 0.52	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)
PER3	period circadian clock 3	1p36.23	7(3/4/0)

SNPs in LD with rs228642 (count: 8) View in gBrowse (chr1:7787776..7823774 )

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]
rs12141033	intron_variant; non_coding_transcript_variant	0.875[CEU]
rs10746473	intron_variant; non_coding_transcript_variant	0.851[CEU]
rs4908482	intron_variant; non_coding_transcript_variant	0.854[CEU]
rs228691	intron_variant; non_coding_transcript_variant	0.849[CEU]
rs228688	intron_variant; non_coding_transcript_variant	0.854[CEU]; 0.816[TSI]
rs7550657	intron_variant; non_coding_transcript_variant	0.954[CEU]
rs228694	intron_variant; non_coding_transcript_variant	0.854[CEU]; 0.819[TSI]
rs228727	intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	0.854[CEU]; 0.819[TSI]

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

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

Reference	Statistical Result	Description	Result Category
Soria, V.,2010	X²-tests:allele P-value > 0.05, genotype P-value > 0.05 in all model	No significant association was observed.	Negative