SNP Report

Basic Info

Name	rs1386494 dbSNP Ensembl
Location	chr12:71958763 - 71958763(1)
Variant Alleles	T/C
Ancestral Allele	T
Minor Allele	T
Minor Allele Frequence	0.143171
Functional Annotation	intron_variant; non_coding_transcript_variant.
Consequence to Transcript	intron_variant(ENST00000333850, ENST00000546576); non_coding_transcript_variant(ENST00000546576)
No. of Studies	3 (Positive: 0; Negative: 3; Trend: 0)
Source	Literature
Overlap with SZ?	NO
Overlap with MDD?	NO

SNP related studies (count: 3)

Reference	Allele Change	Statistical Values	Author Comments	Result Category
Lopez, V. A., 2007	A/G	FBAT P-value = 0.106, Z=-1.616 in the NIMH 'Wave 3' Sample FBAT P-value = 0.106, Z=-1.616 in the NIMH 'Wave 3' Sample	did not show significant association with BPAD or with SA in...... did not show significant association with BPAD or with SA in the individual marker tests More...	Negative
Chen, S., 2014	A/G	Allele frequency: P-value=0.277428, Permutated P-value=0.698...... Allele frequency: P-value=0.277428, Permutated P-value=0.6982; Genotype frequency: P-value=0.440348, H-W P-value=0.603372(case), H-W P-value=0.643185(control). More...	No significant associations were observed. No significant associations were observed.	Negative
Yosifova, A.,2009	T/C	Allelic association: P-value = 0.051 Allelic association: P-value = 0.051	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 rs1386494 (count: 22) View in gBrowse (chr12:71950838..71989834 )

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]
rs1386490	intron_variant; non_coding_transcript_variant	0.918[CEU]
rs4760818	intron_variant	0.919[CEU]
rs1487281	intron_variant	0.913[CEU]
rs1386496	intron_variant; non_coding_transcript_variant	1.0[CEU]
rs10784944	downstream_gene_variant; intron_variant	1.0[CEU]
rs7954568	intron_variant	0.913[CEU]
rs4760814	intron_variant	0.919[CEU]
rs7300490	intron_variant	0.919[CEU]
rs4760751	intron_variant	0.913[CEU]
rs1386488	intron_variant; non_coding_transcript_variant	0.847[CEU]
rs2046582	intron_variant	0.918[CEU]
rs4760749	intron_variant; non_coding_transcript_variant	1.0[CEU]
rs6582072	intron_variant; non_coding_transcript_variant	0.847[CEU]
rs1386489	intron_variant; non_coding_transcript_variant	1.0[CEU]
rs7968346	intron_variant; non_coding_transcript_variant	1.0[CEU]
rs10784942	intron_variant; non_coding_transcript_variant	1.0[CEU]
rs7963226	intron_variant	0.913[CEU]
rs7299582	intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	1.0[CEU]
rs6582081	intron_variant	0.831[CEU]
rs2367899	intron_variant	0.919[CEU]
rs10748189	intron_variant	0.842[CEU]
rs1843812	intron_variant	0.913[CEU]

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

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