SNP Report

Basic Info

Name	rs534654 dbSNP Ensembl
Location	chr4:55424053 - 55424053(1)
Variant Alleles	A/G
Ancestral Allele	G
Minor Allele	A
Minor Allele Frequence	0.13139
Functional Annotation	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant.
Consequence to Transcript	downstream_gene_variant(ENST00000309964); intron_variant(ENST00000381334, ENST00000506103, ENST00000506198, ENST00000508404, ENST00000508561, ENST00000509575, ENST00000514904, ENST00000608091); NMD_transcript_variant(ENST00000506103, ENST00000508404); non_coding_transcript_exon_variant(ENST00000515591); non_coding_transcript_variant(ENST00000508561, ENST00000509575, ENST00000514904, ENST00000515591)
No. of Studies	1 (Positive: 1; Negative: 0; Trend: 0)
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
Shi, J., 2008 (d)	A/G		Allelic TDT P-value = 0.0097 in bipolar disorder (Sample II) Allelic TDT P-value = 0.0097 in bipolar disorder (Sample II)	In Sample II, which is larger, three SNPs (rs534654, rs68505...... In Sample II, which is larger, three SNPs (rs534654, rs6850524, and rs4340844) at the CLOCK gene region showed suggestive evidence for transmission disequilibrium. However, none of these associations reached gene-wide or experiment-wide significance after correction for multiple-testing. More...	Positive

SNP related genes (count: 2)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
TMEM165	transmembrane protein 165	4q12	Mapped by Literature SNP
CLOCK	clock circadian regulator	4q12	12(5/7/0)

SNPs in LD with rs534654 (count: 5) View in gBrowse (chr4:55374120..55424053 )

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]
rs471546	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CEU]
rs504836	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CEU]; 0.957[TSI]
rs4864984	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.933[CEU]; 0.826[TSI]
rs7664496	downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.933[CEU]; 0.826[TSI]
rs549564	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CEU]; 1.0[TSI]

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

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