SNP Report

Basic Info

Name	rs1165678 dbSNP Ensembl
Location	chr12:103928406 - 103928406(1)
Variant Alleles	G/A
Ancestral Allele	A
Minor Allele	G
Minor Allele Frequence	0.228634
Functional Annotation	intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant.
Consequence to Transcript	intron_variant(ENST00000388789); non_coding_transcript_exon_variant(ENST00000548897); non_coding_transcript_variant(ENST00000388789, ENST00000548897); upstream_gene_variant(ENST00000299767, ENST00000540297, ENST00000548462, ENST00000548622, ENST00000549334, ENST00000579335, ENST00000614327)
No. of Studies	1 (Positive: 0; Negative: 1; Trend: 0)
Source	Literature
Overlap with SZ?	YES
Overlap with MDD?	NO

SNP related studies (count: 1)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Kakiuchi, C., 2007 (a)	A/G		chi-square genotypic P-value = 0.67, allelic P-value = 0.908...... chi-square genotypic P-value = 0.67, allelic P-value = 0.9089 for BD cases in MDMD samples; chi-square genotypic P-value = 0.7214, allelic P-value = 0.8165 for BD cases in MPS samples; chi-square genotypic P-value = 0.9817, allelic P-value = 0.8937 for BD cases in total samples. TDT P-value = 0.741 in NIMH trio samples. More...	It was not significantly associated with bipolar disorder an...... It was not significantly associated with bipolar disorder and no significant over transmission was observed in any SNP. More...	Negative

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
HSP90B1	heat shock protein 90kDa beta (Grp94), member 1	12q24.2-q24.3	1(1/0/0)

SNPs in LD with rs1165678 (count: 37) View in gBrowse (chr12:103857394..103998157 )

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: 37)

rs_ID	Functional Annotation	r²[population]
rs10861147	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.926[CHD]; 0.877[JPT]
rs4135079	intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.926[CHD]; 0.877[JPT]
rs11111862	intron_variant; non_coding_transcript_variant	0.877[JPT]
rs4135113	downstream_gene_variant; missense_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.888[CHD]; 0.808[JPT]
rs11111817	non_coding_transcript_exon_variant; non_coding_transcript_variant	0.877[JPT]
rs2293620	5_prime_UTR_variant; downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.926[CHD]; 0.877[JPT]
rs4135054	intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.926[CHD]; 0.877[JPT]
rs3751210	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.844[CHD]; 0.861[JPT]
rs2438116	intron_variant; non_coding_transcript_variant	0.918[JPT]
rs1165677	intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CEU]; 1.0[CHB]; 1.0[JPT]
rs4135126	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.889[CHD]; 0.808[JPT]
rs6539104	intron_variant; non_coding_transcript_variant	0.877[JPT]
rs2722188	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.9[CEU]; 1.0[CHB]
rs3829301	intron_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	0.877[JPT]
rs2251979	intron_variant; non_coding_transcript_variant	0.877[JPT]
rs10507173	downstream_gene_variant; intron_variant	0.924[CHD]; 0.877[JPT]
rs1165666	intron_variant; non_coding_transcript_variant	1.0[CEU]; 1.0[CHB]; 1.0[JPT]
rs12368121	intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[CHD]; 0.933[JPT]
rs4135068	intron_variant; non_coding_transcript_variant	0.83[JPT]
rs7302074	intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs4135109	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.808[JPT]
rs3817602	downstream_gene_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; synonymous_variant	0.889[CHD]; 0.808[JPT]
rs2252000	intron_variant; non_coding_transcript_variant	0.877[JPT]
rs10507172	downstream_gene_variant; intron_variant	0.926[CHD]; 0.877[JPT]
rs10861124	intron_variant; non_coding_transcript_variant	1.0[CHB]; 0.963[CHD]; 1.0[JPT]
rs12368164	intron_variant; non_coding_transcript_variant	0.807[JPT]
rs4135102	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.808[JPT]
rs10861148	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.872[JPT]
rs11111858	intron_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[JPT]
rs2164747	3_prime_UTR_variant; downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	0.877[JPT]
rs2293624	3_prime_UTR_variant; downstream_gene_variant; intron_variant; missense_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	0.891[CHD]; 0.875[JPT]
rs1165682	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.96[CEU]; 1.0[CHB]; 1.0[JPT]
rs10861153	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.889[CHD]; 0.808[JPT]
rs4135115	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.808[JPT]
rs11111865	downstream_gene_variant; intron_variant; upstream_gene_variant	0.808[JPT]
rs1866070	intron_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CEU]; 1.0[CHB]; 1.0[JPT]
rs1183212	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.96[CEU]; 0.976[TSI]; 1.0[CHB]; 1.0[CHD]; 1.0[JPT]

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

Reference	Statistical Result	Description	Result Category
Kakiuchi, C., 2007 (a)	chi-square genotypic P-value = 0.6356, allelic P-value = 0.5415 for SZ cases in total samples	No significant association was observed in single SNPs. However, the result should be treated with caution, because there was a significant difference of gender between patients with schizophrenia and controls.	Negative

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