BDgene

SNP Report

Basic Info
Name rs4680 dbSNP Ensembl
Location chr22:19963748 - 19963748(1)
Variant Alleles G/A
Ancestral Allele G
Minor Allele A
Minor Allele Frequence 0.369209
Functional Annotation downstream_gene_variant; missense_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant.
Polyphen Annotation: possibly damaging(ENST00000403184, ENST00000428707); benign(ENST00000207636, ENST00000361682, ENST00000403710, ENST00000406520, ENST00000407537, ENST00000412786, ENST00000449653)
SIFT Annotation: deleterious(ENST00000403184, ENST00000428707); tolerated(ENST00000207636, ENST00000361682, ENST00000403710, ENST00000406520, ENST00000407537, ENST00000412786, ENST00000449653)
Consequence to Transcript downstream_gene_variant(ENST00000467943); missense_variant(ENST00000207636, ENST00000361682, ENST00000403710, ENST00000406520, ENST00000407537, ENST00000412786, ENST00000449653, ENST00000403184, ENST00000428707); NMD_transcript_variant(ENST00000207636); non_coding_transcript_exon_variant(ENST00000493893); non_coding_transcript_variant(ENST00000493893); upstream_gene_variant(ENST00000585066)
No. of Studies 6 (Positive: 3; Negative: 3; 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
Prata, D. P., 2006 no P-value no P-value A chi-square analysis showed no genotype-wise or allele-wise...... A chi-square analysis showed no genotype-wise or allele-wise association for any individual SNP. More... Positive
Shifman, S., 2004 P-value = 0.34 in the total control, P-value = 0.47 in the n...... P-value = 0.34 in the total control, P-value = 0.47 in the new control of male, P-value = 0.071 in the total control, P-value = 0.12 in the new control of female, P-value = 0.093 in the total control, P-value = 0.19 in the new control of all; OR (95% CI)=1.26 (0.96-1.66) of male, OR (95% CI)=1.42 (1.08-1.87) of female More... the Val/Met polymorphism is not significantly associated wit...... the Val/Met polymorphism is not significantly associated with bipolar disorder More... Negative
Ancin, I.,2011(b) X2 -tests: allele frequency, P-value > 0.05 X2 -tests: allele frequency, P-value > 0.05 No significant association was observed. No significant association was observed. Negative
Funke, B.,2005 A/G Allelic association: for BP, P-value = 0.058, trend P-value ...... Allelic association: for BP, P-value = 0.058, trend P-value = 0.05, OR (95%CI)=1.39(0.99, 1.95); for affective disorder, P-value = 0.018, trend P-value = 0.015, OR (95%CI)=1.43(1.06, 1.93); for all affects, P-value = 0.05, trend P-value = 0.048, OR (95%CI)=1.21(1.00, 1.47) More... No significant association was observed in BP. No significant association was observed in BP. Negative
Massat, I.,2011 A/G For BD: allele, X2=1.92, P-value = 0.16, genotype...... For BD: allele, X2=1.92, P-value = 0.16, genotype, X2=7.43, P-value = 0.02; eraly onset: allele, X2=1.11, P-value = 0.28, genotype, X2=7.37, P-value = 0.01 More... Significant association was found in genotype for BD and ear...... Significant association was found in genotype for BD and early onset BD. More... Positive
Zhang, Z.,2009(b) A/G Allelic association: X2(df)=11.78(1), P-value = 0...... Allelic association: X2(df)=11.78(1), P-value = 0.000603; Genotypic Association: X2(df)=12.41(2), P-value = 0.002033 More... Significant association was observed Significant association was observed Positive

SNP related genes (count: 1)
Approved Symbol Approved Name Location No. of Studies (Positive/Negative/Trend)
COMT catechol-O-methyltransferase 22q11.21 28(14/14/0)

SNPs in LD with rs4680 (count: 3) View in gBrowse (chr22:19961340..19963748 )
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: 3)


Overlap with SZ from cross-disorder studies (count: 2)
Reference Statistical Result Description Result Category
Shifman, S., 2004 OR (95% CI)=1.14 (0.99-1.32) of males, OR (95% CI)=1.09 (0.90-1.32) of females previously found to be associated with schizophrenia Positive
Funke, B.,2005 Allelic association:for SCZ, P-value = 0.419, trend P-value = 0.414, OR (95%CI)=1.1(0.87, 1.41);for SCZ+SA, P-value = 0.304, trend P-value = 0.299, OR (95%CI)=1.12(0.90, 1.40) No significant association was observed in SZ. Negative

Overlap with MDD from cross-disorder studies (count: 2)
Reference Statistical Result Description Result Category
Massat, I.,2011 For MD:allele, X2=0.82, P-value = 0.36, genotype, X2=6.6, P-value = 0.03;eraly onset:allele, X2=0.83, P-value = 0.36, genotype, X2=5.62, P-value = 0.05 Significant association was found in genotype for MD. Positive
Funke, B.,2005 Allelic association:for MDD, P-value = 0.101, trend P-value = 0.093, OR (95%CI)=1.56(0.91, 2.68) No association was observed in MDD. Negative