SNP Report

Basic Info

Name	rs2129575 dbSNP Ensembl
Location	chr12:71946293 - 71946293(1)
Variant Alleles	G/T
Ancestral Allele	G
Minor Allele	T
Minor Allele Frequence	0.333666
Functional Annotation	intron_variant; non_coding_transcript_variant.
Consequence to Transcript	intron_variant(ENST00000333850, ENST00000546576); non_coding_transcript_variant(ENST00000546576)
No. of Studies	2 (Positive: 0; Negative: 2; 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
Van Den Bogaert, A., 2006 (a)	G/T		genotypic P-value = 0.18, allelic P-value = 0.17 genotypic P-value = 0.18, allelic P-value = 0.17		Negative
Roche, S.,2009		T	TDT: X²=3.108, P-value = 0.0779 TDT: X²=3.108, P-value = 0.0779	No significant association was observed No significant association was observed	Negative

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
TPH2	tryptophan hydroxylase 2	12q15	13(10/3/0)

SNPs in LD with rs2129575 (count: 7) View in gBrowse (chr12:71936332..72000519 )

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]
rs11179033	intron_variant	0.839[TSI]
rs11179023	intron_variant	0.839[TSI]
rs12229394	intron_variant	0.842[TSI]
rs10879350	intron_variant	0.839[TSI]
rs6582071	upstream_gene_variant	1.0[CEU]
rs11834114	intron_variant	0.839[TSI]
rs11179027	intron_variant	0.839[TSI]

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

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

Reference	Statistical Result	Description	Result Category
Van Den Bogaert, A., 2006 (a)	genotypic P-value = 0.43, allelic P-value = 0.43		Negative