SNP Report

Basic Info

Name	rs1042779 dbSNP Ensembl
Location	chr3:52786995 - 52786995(1)
Variant Alleles	A/G
Ancestral Allele	G
Minor Allele	G
Minor Allele Frequence	0.42472
Functional Annotation	downstream_gene_variant; missense_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant. Polyphen Annotation: benign(ENST00000273283, ENST00000428133, ENST00000484844, ENST00000537050) SIFT Annotation: tolerated(ENST00000273283, ENST00000428133, ENST00000484844, ENST00000537050)
Consequence to Transcript	downstream_gene_variant(ENST00000478667, ENST00000487686, ENST00000494603); missense_variant(ENST00000273283, ENST00000428133, ENST00000484844, ENST00000537050); NMD_transcript_variant(ENST00000484844); non_coding_transcript_exon_variant(ENST00000628722); non_coding_transcript_variant(ENST00000628722); upstream_gene_variant(ENST00000405128, ENST00000482836, ENST00000494705)
No. of Studies	2 (Positive: 1; Negative: 0; Trend: 1)
Source	Literature
Overlap with SZ?	YES
Overlap with MDD?	NO

SNP related studies (count: 2)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Kondo, K.,2013	A/G		P-value = 0.025,OR= 1.14 P-value = 0.025,OR= 1.14	Significant association was observed. Significant association was observed.	Positive
Scott, L. J.,2009	A/G		NIMH/Pritzker: OR (95% CI)=1.2(1.04-1.38), P-value = 0.015; ...... NIMH/Pritzker: OR (95% CI)=1.2(1.04-1.38), P-value = 0.015; GSK(reduced sample): OR (95% CI)=1.31(1.11-1.54), P-value = 0.0012; WTCCC: OR (95% CI)=1.16(1.07-1.25), P-value = 0.00012; 3-study meta-analysis: OR (95% CI)=1.19(1.11-1.27), P-value = 0.00000018; Heterogeneity: I²%=0, P-value = 0.4 More...		Trend

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
ITIH1	inter-alpha-trypsin inhibitor heavy chain 1	3p21.1	1(1/0/0)

SNPs in LD with rs1042779 (count: 91) View in gBrowse (chr3:52587823..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: 91)

rs_ID	Functional Annotation	r²[population]
rs2083180	intron_variant; NMD_transcript_variant	0.83[CHB]; 0.86[JPT]
rs2071506	downstream_gene_variant; upstream_gene_variant	0.811[CEU]; 0.829[TSI]; 0.817[CHB]; 0.923[CHD]; 0.906[JPT]
rs3852066	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.825[TSI]; 0.83[CHB]; 0.86[JPT]
rs6976	3_prime_UTR_variant; downstream_gene_variant; NMD_transcript_variant	0.844[TSI]; 0.83[CHB]; 0.86[JPT]
rs13082960	intron_variant; NMD_transcript_variant; upstream_gene_variant	0.857[JPT]
rs2118540	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.805[JPT]
rs2336146	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.825[TSI]; 0.83[CHB]; 0.86[JPT]
rs3774355	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.902[CEU]; 0.862[CHB]; 0.86[JPT]
rs2286798	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.951[CEU]; 0.977[TSI]; 0.91[CHB]; 0.949[CHD]; 0.953[JPT]
rs7624716	intron_variant	0.825[TSI]; 0.83[CHB]; 0.86[JPT]
rs1014969	upstream_gene_variant	0.83[CHB]; 0.86[JPT]
rs13079063	3_prime_UTR_variant; downstream_gene_variant; upstream_gene_variant	0.819[TSI]; 0.821[CHB]; 0.903[JPT]
rs10510760	intron_variant; NMD_transcript_variant; upstream_gene_variant	0.83[CHB]; 0.86[JPT]
rs12635140	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.825[TSI]; 0.83[CHB]; 0.86[JPT]
rs4687551	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.811[CEU]; 0.805[TSI]; 0.862[CHB]; 0.923[CHD]; 0.86[JPT]
rs6445535	downstream_gene_variant; intron_variant	0.825[TSI]; 0.83[CHB]; 0.86[JPT]
rs2268023	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.862[CHB]; 0.906[JPT]
rs2164884	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.861[TSI]; 0.823[CHB]; 0.901[JPT]
rs11177	downstream_gene_variant; missense_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.844[TSI]; 0.83[CHB]; 0.814[JPT]
rs11130323	downstream_gene_variant; intron_variant	0.83[CHB]; 0.86[JPT]
rs4687548	intron_variant; NMD_transcript_variant	0.83[CHB]; 0.86[JPT]
rs1075653	downstream_gene_variant; intron_variant; non_coding_transcript_variant; splice_region_variant; upstream_gene_variant	0.811[CEU]; 0.827[TSI]; 0.862[CHB]; 0.923[CHD]; 0.906[JPT]
rs2071044	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.866[CHB]
rs9881468	downstream_gene_variant; upstream_gene_variant	0.811[CEU]; 0.862[CHB]; 0.899[CHD]; 0.906[JPT]
rs9324	downstream_gene_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; synonymous_variant; upstream_gene_variant	0.811[CEU]; 0.827[TSI]; 0.859[CHB]; 0.923[CHD]; 0.906[JPT]
rs2268027	downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.813[CHB]; 0.85[JPT]
rs4481150	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.807[CHB]; 0.812[JPT]
rs2240919	downstream_gene_variant; intron_variant; upstream_gene_variant	0.91[CHB]; 0.903[JPT]
rs8906	5_prime_UTR_variant; downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.844[TSI]; 0.83[CHB]; 0.86[JPT]
rs12497998	downstream_gene_variant; intron_variant	0.825[TSI]; 0.83[CHB]; 0.86[JPT]
rs3774354	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.904[CEU]; 0.977[TSI]; 0.862[CHB]; 0.897[CHD]; 0.906[JPT]
rs2159644	downstream_gene_variant; intron_variant	0.825[TSI]; 0.83[CHB]; 0.86[JPT]
rs2535627	downstream_gene_variant	0.826[CHB]
rs2164885	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.823[TSI]; 0.822[CHB]; 0.903[JPT]
rs3733039	intron_variant; upstream_gene_variant	0.825[TSI]; 0.83[CHB]; 0.86[JPT]
rs11717836	upstream_gene_variant	0.813[CHB]; 0.847[JPT]
rs10780035	intron_variant; upstream_gene_variant	0.844[TSI]; 0.83[CHB]; 0.86[JPT]
rs2336545	intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.866[TSI]; 0.83[CHB]; 0.86[JPT]
rs11130312	intron_variant; NMD_transcript_variant	0.83[CHB]; 0.86[JPT]
rs2071507	downstream_gene_variant; upstream_gene_variant	0.811[CEU]; 0.91[CHB]; 0.953[JPT]
rs678	downstream_gene_variant; missense_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.951[CEU]; 0.91[CHB]; 0.953[JPT]
rs2240920	downstream_gene_variant; intron_variant; upstream_gene_variant	0.904[CEU]; 0.91[CHB]; 0.949[CHD]; 0.953[JPT]
rs2071508	downstream_gene_variant; upstream_gene_variant	0.808[CEU]; 0.829[TSI]; 0.856[CHB]; 0.923[CHD]; 0.906[JPT]
rs767418	downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.823[TSI]; 0.83[CHB]; 0.854[JPT]
rs11130310	intron_variant; NMD_transcript_variant	0.825[TSI]; 0.83[CHB]; 0.813[JPT]
rs35526119	downstream_gene_variant; intron_variant	0.825[TSI]; 0.83[CHB]; 0.86[JPT]
rs4687550	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.811[CEU]; 0.862[CHB]; 0.906[JPT]
rs6778329	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.903[CHB]; 0.949[JPT]
rs1029871	downstream_gene_variant; missense_variant	0.83[CHB]; 0.86[JPT]
rs6804145	downstream_gene_variant; intron_variant; NMD_transcript_variant	0.823[TSI]; 0.83[CHB]; 0.86[JPT]
rs998909	upstream_gene_variant	0.823[CHB]; 0.899[JPT]
rs2239699	downstream_gene_variant; upstream_gene_variant	0.904[CEU]; 0.893[CHB]; 0.888[JPT]
rs2239551	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.816[CEU]; 0.955[TSI]; 0.859[CHB]; 0.923[CHD]; 0.906[JPT]
rs13085895	intron_variant; NMD_transcript_variant	0.83[CHB]; 0.86[JPT]
rs10865973	intron_variant; upstream_gene_variant	0.83[CHB]; 0.86[JPT]
rs3617	downstream_gene_variant; missense_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.911[CHB]; 0.816[JPT]
rs3774366	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.825[TSI]; 0.83[CHB]; 0.86[JPT]
rs2270197	downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.862[CHB]; 0.906[JPT]
rs2028216	downstream_gene_variant; intron_variant; NMD_transcript_variant	0.844[TSI]; 0.83[CHB]; 0.86[JPT]
rs13071584	intron_variant; NMD_transcript_variant	0.825[TSI]; 0.83[CHB]; 0.86[JPT]
rs6445534	3_prime_UTR_variant; downstream_gene_variant; upstream_gene_variant	0.83[CHB]; 0.818[JPT]
rs2239549	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.859[CEU]; 0.955[TSI]; 0.819[CHB]; 0.923[CHD]; 0.906[JPT]
rs9879090	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.822[CHB]; 0.867[JPT]
rs4687638	intron_variant; NMD_transcript_variant; upstream_gene_variant	0.844[TSI]; 0.83[CHB]; 0.86[JPT]
rs6762813	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.844[TSI]; 0.83[CHB]; 0.86[JPT]
rs3755798	downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.825[TSI]; 0.86[JPT]
rs13082208	intron_variant; NMD_transcript_variant; upstream_gene_variant	0.856[CHB]; 0.891[JPT]
rs1866268	intron_variant; upstream_gene_variant	0.825[TSI]; 0.83[CHB]; 0.86[JPT]
rs11716747	downstream_gene_variant; intron_variant	0.822[TSI]; 0.83[CHB]; 0.86[JPT]
rs3774365	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.83[CHB]; 0.86[JPT]
rs12488461	downstream_gene_variant; intron_variant; NMD_transcript_variant	0.857[JPT]
rs34017441	3_prime_UTR_variant; downstream_gene_variant; upstream_gene_variant	0.866[TSI]; 0.83[CHB]; 0.906[JPT]
rs2276824	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.83[CHB]; 0.867[JPT]
rs2019065	upstream_gene_variant	0.977[TSI]; 1.0[CHB]; 0.974[CHD]; 0.953[JPT]
rs3733041	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.825[TSI]; 0.83[CHB]; 0.86[JPT]
rs2268025	intron_variant	0.866[CHB]; 0.86[JPT]
rs2072390	intron_variant; NMD_transcript_variant; upstream_gene_variant	0.8[TSI]; 0.83[CHB]; 0.857[JPT]
rs2577831	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.83[CHB]; 0.867[JPT]
rs7622694	intron_variant; NMD_transcript_variant	0.825[TSI]; 0.83[CHB]; 0.86[JPT]
rs11714419	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.844[TSI]; 0.83[CHB]; 0.86[JPT]
rs6617	5_prime_UTR_variant; downstream_gene_variant; intron_variant; missense_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.83[CHB]; 0.86[JPT]
rs2710323	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.954[CHB]; 0.903[CHD]; 0.909[JPT]
rs2300149	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.859[CEU]; 0.955[TSI]; 0.862[CHB]; 0.923[CHD]; 0.906[JPT]
rs2590838	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.83[CHB]; 0.867[JPT]
rs1108842	5_prime_UTR_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.83[CHB]; 0.867[JPT]
rs1076425	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.811[CEU]; 0.829[TSI]; 0.862[CHB]; 0.923[CHD]; 0.906[JPT]
rs2079929	intron_variant; upstream_gene_variant	0.825[TSI]; 0.83[CHB]; 0.86[JPT]
rs3755799	upstream_gene_variant	0.83[CHD]
rs13083798	intron_variant; NMD_transcript_variant; upstream_gene_variant	0.826[CHB]; 0.907[JPT]
rs2230535	downstream_gene_variant; synonymous_variant	0.866[TSI]; 0.83[CHB]; 0.86[JPT]
rs3733045	intron_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	0.825[TSI]; 0.83[CHB]; 0.86[JPT]

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

Reference	Statistical Result	Description	Result Category
Kondo, K.,2013	P-value = 0.012,OR= 1.16	Significant association was observed.	Positive

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