SNP Report

Basic Info

Name	rs140504 dbSNP Ensembl
Location	chr22:23285182 - 23285182(1)
Variant Alleles	A/G
Ancestral Allele	G
Minor Allele	A
Minor Allele Frequence	0.20627
Functional Annotation	downstream_gene_variant; intron_variant; missense_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant. Polyphen Annotation: benign(ENST00000305877, ENST00000359540) SIFT Annotation: tolerated(ENST00000305877, ENST00000359540)
Consequence to Transcript	downstream_gene_variant(ENST00000427791); intron_variant(ENST00000398512); missense_variant(ENST00000305877, ENST00000359540); non_coding_transcript_exon_variant(ENST00000466076, ENST00000487968); non_coding_transcript_variant(ENST00000466076, ENST00000487968); upstream_gene_variant(ENST00000419722)
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
Yosifova, A.,2009	G/A		Allelic association: P-value = 0.9 Allelic association: P-value = 0.9	No significant association was observed No significant association was observed	Negative
Hashimoto, R.,2005(a)	A/G		Allelic association: for BP, P-value = 0.0054, OR=1.45; for ...... Allelic association: for BP, P-value = 0.0054, OR=1.45; for BPII, P-value = 0.0014, OR=1.84; for total cases, P-value = 0.018, OR=1.26; genotypic association: for BPII, P-value = 0.0046; OR(95%CI)=3.10(1.53-8.76) More...	Significant associations were found in BD. Significant associations were found in BD.	Positive

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
BCR	breakpoint cluster region	22q11	2(1/1/0)

SNPs in LD with rs140504 (count: 3) View in gBrowse (chr22:23244758..23285182 )

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]
rs3788359	intron_variant	0.87[CHB]; 0.823[JPT]
rs5751613	intron_variant; non_coding_transcript_variant	0.843[CHD]
rs5759660	intron_variant; non_coding_transcript_variant	0.823[CHD]

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

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

Reference	Statistical Result	Description	Result Category
Hashimoto, R.,2005(a)	Allelic association:for MDD, P-value > 0.05	No significant associations were found in MDD.	Negative