SNP Report

Basic Info

Name	rs1843809 dbSNP Ensembl
Location	chr12:71954918 - 71954918(1)
Variant Alleles	G/T
Ancestral Allele	G
Minor Allele	G
Minor Allele Frequence	0.203075
Functional Annotation	intron_variant; non_coding_transcript_variant.
Consequence to Transcript	intron_variant(ENST00000333850, ENST00000546576); non_coding_transcript_variant(ENST00000546576)
No. of Studies	4 (Positive: 1; Negative: 3; Trend: 0)
Source	Literature
Overlap with SZ?	NO
Overlap with MDD?	YES

SNP related studies (count: 4)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Cichon, S., 2008	T/G	G	Cochrane-Armitage trend test P-value > .0.5 in the German BP...... Cochrane-Armitage trend test P-value > .0.5 in the German BPAD sample. Cochrane-Armitage trend test P-value = 0.26 in the Russian BPAD sample. Cochrane-Armitage trend test P-value > .0.5 in Combined German/Russian sample. More...		Positive
Grigoroiu-Serbanescu, M.,2008	T/G		Cochrane-Armitage trend test P value=0.462 Cochrane-Armitage trend test P value=0.462		Negative
Roche, S.,2009		G	TDT: X²=0.222, P-value = 0.6374 TDT: X²=0.222, P-value = 0.6374	No significant association was observed No significant association was observed	Negative
Van Den Bogaert, A., 2006 (a)	G/T		genotypic P-value = 0.25, allelic P-value = 0.23 genotypic P-value = 0.25, allelic P-value = 0.23		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 rs1843809 (count: 23) View in gBrowse (chr12:71950838..72004337 )

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]
rs7954568	intron_variant	0.906[CEU]
rs1386496	intron_variant; non_coding_transcript_variant	1.0[CEU]; 1.0[TSI]
rs1843812	intron_variant	0.913[CEU]; 0.96[TSI]
rs4760814	intron_variant	0.913[CEU]
rs10748189	intron_variant	0.831[CEU]
rs1386489	intron_variant; non_coding_transcript_variant	1.0[CEU]; 1.0[TSI]
rs2046582	intron_variant	0.912[CEU]
rs4760751	intron_variant	0.913[CEU]; 1.0[TSI]
rs6582072	intron_variant; non_coding_transcript_variant	0.847[CEU]
rs1487281	intron_variant	0.913[CEU]; 1.0[TSI]
rs7299582	intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	1.0[CEU]; 1.0[TSI]
rs10784942	intron_variant; non_coding_transcript_variant	1.0[CEU]
rs7300490	intron_variant	0.913[CEU]
rs2367899	intron_variant	0.913[CEU]
rs1386490	intron_variant; non_coding_transcript_variant	0.912[CEU]
rs1386488	intron_variant; non_coding_transcript_variant	0.847[CEU]
rs7968346	intron_variant; non_coding_transcript_variant	1.0[CEU]
rs4760749	intron_variant; non_coding_transcript_variant	1.0[CEU]
rs7963226	intron_variant	0.913[CEU]; 1.0[TSI]
rs990234	intron_variant	0.831[CEU]
rs6582081	intron_variant	0.831[CEU]; 1.0[TSI]
rs4760818	intron_variant	0.913[CEU]
rs10784944	downstream_gene_variant; intron_variant	1.0[CEU]; 1.0[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 = 0.81, allelic P-value = 0.78		Negative