SNP Report

Basic Info

Name	rs736408 dbSNP Ensembl
Location	chr3:52801338 - 52801338(1)
Variant Alleles	C/T
Ancestral Allele	T
Minor Allele	T
Minor Allele Frequence	0.489217
Functional Annotation	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant.
Consequence to Transcript	downstream_gene_variant(ENST00000463893, ENST00000465243); intron_variant(ENST00000416872, ENST00000449956, ENST00000464804, ENST00000621946); non_coding_transcript_variant(ENST00000464804); upstream_gene_variant(ENST00000465314, ENST00000475931, ENST00000493136, ENST00000495622)
No. of Studies	3 (Positive: 1; Negative: 0; Trend: 2)
Source	Literature
Overlap with SZ?	YES
Overlap with MDD?	NO

SNP related studies (count: 3)

Reference	Allele Change	Statistical Values	Author Comments	Result Category
Green, E. K.,2012	C/T	BD ImmunoChip:P-value = 0.0756,OR = 1.098;ImmunoChip, PGC-BD...... BD ImmunoChip:P-value = 0.0756,OR = 1.098;ImmunoChip, PGC-BD combined data:P-balue = 0.000000503,OR = 1.1 More...	Suggestive association was found. Suggestive association was found.	Trend
Sklar, P.,2011	C/T	Primary GWAS P-value(GC)=0.00000122, OR=1.14; replication P-...... Primary GWAS P-value(GC)=0.00000122, OR=1.14; replication P-value(1-sided)=0.0465, OR=1.05; Combined GWAS and replication P-value(GC)=0.00000219, OR=1.1 More...	Suggestive association was found. Suggestive association was found.	Trend
Kondo, K.,2013	A/G	P-value = 0.034,OR= 0.885 P-value = 0.034,OR= 0.885	Significant association was observed. Significant association was observed.	Positive

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
ITIH3	inter-alpha-trypsin inhibitor heavy chain 3	3p21.1	3(3/0/0)

SNPs in LD with rs736408 (count: 34) View in gBrowse (chr3:52697253..52813585 )

The LD data used here is based on HapMap rel#27. LD SNP pairs were selected with a threshold r²<=0.8.

Literature-origin SNPs (count: 0)

LD-proxies (count: 34)

rs_ID	Functional Annotation	r²[population]
rs2071506	downstream_gene_variant; upstream_gene_variant	0.811[CEU]; 0.863[CHB]; 0.908[JPT]
rs2268023	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.915[CHB]; 0.912[JPT]
rs2535627	downstream_gene_variant	0.867[CHB]; 0.866[JPT]
rs4687550	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.826[CEU]; 0.915[CHB]; 0.912[JPT]
rs13079063	3_prime_UTR_variant; downstream_gene_variant; upstream_gene_variant	0.81[JPT]
rs4481150	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.807[CHB]; 0.902[JPT]
rs3774355	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.915[CHB]; 0.874[JPT]
rs2071507	downstream_gene_variant; upstream_gene_variant	0.826[CEU]; 0.875[CHB]; 0.868[JPT]
rs1075653	downstream_gene_variant; intron_variant; non_coding_transcript_variant; splice_region_variant; upstream_gene_variant	0.811[CEU]; 0.91[CHB]; 0.908[JPT]
rs2300149	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.91[CHB]; 0.908[JPT]
rs2239699	downstream_gene_variant; upstream_gene_variant	0.897[CHB]; 0.897[JPT]
rs2268025	intron_variant	0.822[CHB]
rs3617	downstream_gene_variant; missense_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.863[CHB]; 0.905[JPT]
rs2270197	downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.815[CEU]; 0.915[CHB]; 0.912[JPT]
rs2240920	downstream_gene_variant; intron_variant; upstream_gene_variant	0.868[CHB]; 0.859[JPT]
rs1076425	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.811[CEU]; 0.91[CHB]; 0.908[JPT]
rs34017441	3_prime_UTR_variant; downstream_gene_variant; upstream_gene_variant	0.816[JPT]
rs3774354	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.91[CHB]; 0.908[JPT]
rs2286798	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.868[CHB]; 0.859[JPT]
rs2710323	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CHB]; 0.826[JPT]
rs2019065	upstream_gene_variant	0.954[CHB]; 0.859[JPT]
rs2071044	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.909[CHB]; 0.863[JPT]
rs2071508	downstream_gene_variant; upstream_gene_variant	0.808[CEU]; 0.907[CHB]; 0.908[JPT]
rs2164885	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.812[JPT]
rs9324	downstream_gene_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; synonymous_variant; upstream_gene_variant	0.811[CEU]; 0.908[CHB]; 0.908[JPT]
rs9881468	downstream_gene_variant; upstream_gene_variant	0.811[CEU]; 0.91[CHB]; 0.908[JPT]
rs6778329	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.866[CHB]; 0.856[JPT]
rs13082208	intron_variant; NMD_transcript_variant; upstream_gene_variant	0.809[CHB]; 0.896[JPT]
rs2239549	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.868[CHB]; 0.908[JPT]
rs4687551	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.811[CEU]; 0.91[CHB]; 0.866[JPT]
rs2240919	downstream_gene_variant; intron_variant; upstream_gene_variant	0.875[CHB]; 0.823[JPT]
rs678	downstream_gene_variant; missense_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.875[CHB]; 0.865[JPT]
rs998909	upstream_gene_variant	0.808[JPT]
rs2239551	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.908[CHB]; 0.908[JPT]

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

Reference	Statistical Result	Description	Result Category
Kondo, K.,2013	P-value = 0.021,OR= 0.874	Significant association was observed.	Positive

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