SNP Report

Basic Info

Name	rs6023059 dbSNP Ensembl
Location	chr20:38109369 - 38109369(1)
Variant Alleles	T/C
Ancestral Allele	C
Minor Allele	T
Minor Allele Frequence	0.360623
Functional Annotation	intron_variant; non_coding_transcript_variant; upstream_gene_variant.
Consequence to Transcript	intron_variant(ENST00000614670, ENST00000618318); non_coding_transcript_variant(ENST00000618318); upstream_gene_variant(ENST00000615357)
No. of Studies	1 (Positive: 1; Negative: 0; Trend: 0)
Source	Literature
Overlap with SZ?	NO
Overlap with MDD?	NO

SNP related studies (count: 1)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Graae, L.,2012	C/T		Association analysis: for female, P-value corrected with Bon...... Association analysis: for female, P-value corrected with Bonferroni correction=0.023; ; odds ratio (OR) 0.681, 95% confidence interval (CI) 0.570-0.814 More...	Significant association was observed in BD. Significant association was observed in BD.	Positive

SNP related genes (count: 2)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
RPRD1B	regulation of nuclear pre-mRNA domain containing 1B	20q11.23	Mapped by Literature SNP
TGM2	transglutaminase 2	20q12	1(1/0/0)

SNPs in LD with rs6023059 (count: 9) View in gBrowse (chr20:37983262..38109720 )

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]
rs6022716	downstream_gene_variant; intron_variant; NMD_transcript_variant	1.0[CEU]; 0.977[TSI]
rs6013677	intron_variant	1.0[CEU]
rs910664	intron_variant; NMD_transcript_variant	1.0[CEU]; 0.977[TSI]
rs909859	intron_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CEU]
rs6022212	intron_variant	1.0[CEU]; 0.977[TSI]
rs2037	3_prime_UTR_variant	1.0[CEU]; 0.977[TSI]
rs6013590	intron_variant	1.0[CEU]; 0.977[TSI]
rs6022787	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CEU]
rs6097507	intron_variant; NMD_transcript_variant	1.0[CEU]; 0.977[TSI]

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

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