SNP Report

Basic Info

Name	rs12648271 dbSNP Ensembl
Location	chr4:55501955 - 55501955(1)
Variant Alleles	G/C
Ancestral Allele	G
Minor Allele	C
Minor Allele Frequence	0.301518
Functional Annotation	intron_variant; non_coding_transcript_variant; upstream_gene_variant.
Consequence to Transcript	intron_variant(ENST00000309964, ENST00000381322, ENST00000435527, ENST00000506747, ENST00000506923, ENST00000509151, ENST00000513033, ENST00000513440); non_coding_transcript_variant(ENST00000506747, ENST00000506923, ENST00000509151, ENST00000513033); upstream_gene_variant(ENST00000459424)
No. of Studies	2 (Positive: 2; Negative: 0; Trend: 0)
Source	Literature
Overlap with SZ?	NO
Overlap with MDD?	NO

SNP related studies (count: 2)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Dmitrzak-Weglarz, M. P., 2014	G/C		BPD: P-value=0.0353, FDR=0.3253, OR=0.82, 95%CI=0.68-0.99; B...... BPD: P-value=0.0353, FDR=0.3253, OR=0.82, 95%CI=0.68-0.99; BPDII: P-value=0.0311, FDR=0.1642, OR=0.71, 95%CI=0.51-0.98. More...	Significant association was observed. Significant association was observed.	Positive
Kripke, D. F.,2009	C/G		TDT: In BP: OR=1.247, CHISQ=4.951, P-value = 0.0261, empiric...... TDT: In BP: OR=1.247, CHISQ=4.951, P-value = 0.0261, empirical P-value = 0.0369, corrected empirical P-value = 0.9806 More...	Significant association was observed in the BP group. Significant association was observed in the BP group.	Positive

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
CLOCK	clock circadian regulator	4q12	12(5/7/0)

SNPs in LD with rs12648271 (count: 22) View in gBrowse (chr4:55401306..55577294 )

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: 22)

rs_ID	Functional Annotation	r²[population]
rs13132420	intron_variant; non_coding_transcript_variant	0.828[CEU]
rs4864996	3_prime_UTR_variant; downstream_gene_variant; intron_variant; upstream_gene_variant	0.834[CEU]
rs2035691	intron_variant; non_coding_transcript_variant	0.833[CEU]
rs2171618	intron_variant	0.828[CEU]
rs12500686	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.863[CEU]
rs13116035	intron_variant	0.834[CEU]
rs12649507	intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.828[CEU]
rs4864543	intron_variant; non_coding_transcript_variant	0.86[CEU]
rs12641881	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CEU]
rs1522114	intron_variant; non_coding_transcript_variant	0.828[CEU]
rs6843722	intron_variant; non_coding_transcript_variant	0.834[CEU]
rs6849474	3_prime_UTR_variant; downstream_gene_variant; intron_variant; missense_variant; NMD_transcript_variant; upstream_gene_variant	0.834[CEU]
rs12510400	intron_variant	0.834[CEU]
rs11945371	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.828[CEU]
rs13124436	intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.815[CEU]
rs2272073	intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.828[CEU]
rs11133377	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CEU]
rs7658446	intron_variant; non_coding_transcript_variant	0.833[CEU]
rs13140173	intron_variant; non_coding_transcript_variant	0.887[CEU]
rs13120134	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CEU]
rs11943206	intron_variant	0.828[CEU]
rs2048564	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.828[CEU]

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

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