SNP Report

Basic Info

Name	rs766288 dbSNP Ensembl
Location	chr1:231557942 - 231557942(1)
Variant Alleles	G/T
Ancestral Allele	G
Minor Allele	T
Minor Allele Frequence	0.417133
Functional Annotation	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant.
Consequence to Transcript	downstream_gene_variant(ENST00000602825); intron_variant(ENST00000366639, ENST00000413309, ENST00000475168, ENST00000602567, ENST00000602634, ENST00000602885, ENST00000602956, ENST00000602962); NMD_transcript_variant(ENST00000602567, ENST00000602634, ENST00000602885, ENST00000602956, ENST00000602962); non_coding_transcript_variant(ENST00000475168)
No. of Studies	4 (Positive: 1; Negative: 3; Trend: 0)
Source	Literature
Overlap with SZ?	YES
Overlap with MDD?	YES

SNP related studies (count: 4)

Reference	Allele Change	Statistical Values	Author Comments	Result Category
Ram Murthy, A., 2012		BPAD patients: P-value=0.074, P-value=0.004 for females, P-v...... BPAD patients: P-value=0.074, P-value=0.004 for females, P-value=0.0902 for males; BPAD&SCZ: P-value=0.336, P-value=0.004 for females, P-value=0.248 for males More...	The most significant association was found for rs766288 with...... The most significant association was found for rs766288 with BPAD females. More...	Positive
Schosser, A., 2010	A/C	genotypic/allelic test P-value = 0.15/0.06 genotypic/allelic test P-value = 0.15/0.06	No significant genotypic or allelic association was observed...... No significant genotypic or allelic association was observed. More...	Negative
Okuda, A.,2010	C/T	chi square test: genotype P-value = 0.0572, allele P-value =...... chi square test: genotype P-value = 0.0572, allele P-value = 0.778 More...	No significant association was observed in BD. No significant association was observed in BD.	Negative
Thomson, P. A.,2005(a)		Single-Marker Analysis: allele frequency, for BP, P-value = ...... Single-Marker Analysis: allele frequency, for BP, P-value = 0.71 More...	No significant association was observed. No significant association was observed.	Negative

SNP related genes (count: 2)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
TSNAX	translin-associated factor X	1q42.2	4(3/1/0)
DISC1	disrupted in schizophrenia 1	1q42.1	18(10/7/1)

SNPs in LD with rs766288 (count: 11) View in gBrowse (chr1:231520672..231594375 )

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]
rs1655305	intron_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	0.835[CEU]
rs1765782	intron_variant; NMD_transcript_variant	0.957[CEU]; 0.831[CHB]; 0.894[JPT]
rs1765791	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.84[CEU]
rs1655288	intron_variant; NMD_transcript_variant	0.85[CEU]
rs1619386	intron_variant; NMD_transcript_variant	0.835[CEU]
rs3125933	downstream_gene_variant; intron_variant; NMD_transcript_variant	0.848[CEU]
rs7533573	intron_variant; NMD_transcript_variant	0.957[CEU]; 0.891[CHB]; 0.894[JPT]
rs1982095	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.96[CEU]; 0.946[CHB]; 0.947[JPT]
rs2808579	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CEU]
rs1765794	downstream_gene_variant	0.806[CEU]
rs1612154	downstream_gene_variant; intron_variant; NMD_transcript_variant	0.828[CEU]

Overlap with SZ from cross-disorder studies (count: 2)

Reference	Statistical Result	Description	Result Category
Thomson, P. A.,2005(a)	Single-Marker Analysis:allele frequency, for SZ, P-value = 0.72	No significant association was observed.	Negative
Ram Murthy, A., 2012	SZ patients: P-value=0.906, P-value=0.03 for females, P-value=0.105 for males; BPAD&SCZ: P-value=0.336, P-value=0.004 for females, P-value=0.248 for males	The most significant association was found for combined female cases of BPAD or SCZ. Moderate associations were also observed in females for rs766288 (SCZ, P=0.03)	Positive

Overlap with MDD from cross-disorder studies (count: 2)

Reference	Statistical Result	Description	Result Category
Okuda, A.,2010	chi square test:genotype P-value = 0.0742, allele P-value = 0.0727	No significant association was observed.	Negative
Schosser, A., 2010	genotypic/allelic test P-value: 0.27/0.15	No significant genotypic or allelic association was observed.	Negative