SNP Report

Basic Info

Name	rs821597 dbSNP Ensembl
Location	chr1:231966518 - 231966518(1)
Variant Alleles	G/A
Ancestral Allele	A
Minor Allele	G
Minor Allele Frequence	0.479233
Functional Annotation	intron_variant; NMD_transcript_variant; non_coding_transcript_variant.
Consequence to Transcript	intron_variant(ENST00000366637, ENST00000422590, ENST00000427560, ENST00000439617, ENST00000535983, ENST00000620189, ENST00000622252); NMD_transcript_variant(ENST00000422590); non_coding_transcript_variant(ENST00000427560)
No. of Studies	3 (Positive: 0; Negative: 3; Trend: 0)
Source	Literature
Overlap with SZ?	YES
Overlap with MDD?	YES

SNP related studies (count: 3)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Schosser, A., 2010	C/T		genotypic/allelic test P-value = 0.87/0.94 genotypic/allelic test P-value = 0.87/0.94	No significant genotypic or allelic association was observed...... No significant genotypic or allelic association was observed. More...	Negative
Xiao, Y.,2011	A/G	A	Allelic permutated P-value = 0.998, genotypic permutated P-...... Allelic permutated P-value = 0.998, genotypic permutated P-value = 0.266 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 = 0.67 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 rs821597 (count: 14) View in gBrowse (chr1:231958983..232011854 )

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]
rs864752	downstream_gene_variant; intron_variant	0.96[CEU]; 0.892[TSI]; 0.951[CHB]; 0.926[CHD]; 0.851[JPT]
rs2794273	3_prime_UTR_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.844[TSI]
rs821600	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CEU]; 1.0[TSI]; 1.0[CHB]; 1.0[CHD]; 0.905[JPT]
rs821664	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.959[CEU]
rs849349	downstream_gene_variant; intron_variant	0.954[CEU]; 0.948[CHB]; 0.843[JPT]
rs821624	downstream_gene_variant; intron_variant	0.959[CEU]; 0.951[CHB]; 0.841[JPT]
rs701161	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CEU]; 0.95[CHB]; 0.851[JPT]
rs821627	downstream_gene_variant; intron_variant	0.96[CEU]; 0.946[TSI]; 0.9[CHB]; 0.859[CHD]; 0.812[JPT]
rs821655	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.959[CEU]
rs843979	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.96[CEU]; 0.825[TSI]
rs1754607	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CEU]; 1.0[CHB]; 0.925[CHD]; 0.95[JPT]
rs821662	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.92[CEU]; 0.815[TSI]
rs701162	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.917[CEU]
rs821654	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.96[CEU]; 0.841[TSI]

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

Reference	Statistical Result	Description	Result Category
Thomson, P. A.,2005(a)	Single-Marker Analysis:allele frequency, for SZ, P-value = 0.16	No significant association was observed.	Negative

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

Reference	Statistical Result	Description	Result Category
Schosser, A., 2010	genotypic/allelic test P-value: 0.40/0.28	No significant genotypic or allelic association was observed.	Negative