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	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)

rs_ID	Functional Annotation	r²[population]
rs740601	downstream_gene_variant; intron_variant; NMD_transcript_variant; upstream_gene_variant	0.815[TSI]
rs165656	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CEU]; 0.934[TSI]; 0.936[CHB]; 0.944[CHD]; 0.935[JPT]
rs2239393	downstream_gene_variant; intron_variant; NMD_transcript_variant; upstream_gene_variant	0.815[TSI]

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