SNP Report

Basic Info

Name	rs602104 dbSNP Ensembl
Location	chr11:120938674 - 120938674(1)
Variant Alleles	T/C
Ancestral Allele	T
Minor Allele	C
Minor Allele Frequence	0.107428
Functional Annotation	intron_variant; non_coding_transcript_variant; upstream_gene_variant.
Consequence to Transcript	intron_variant(ENST00000438375, ENST00000527524, ENST00000533291); non_coding_transcript_variant(ENST00000533291); upstream_gene_variant(ENST00000532126)
No. of Studies	1 (Positive: 1; Negative: 0; 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
Pickard, B. S., 2006	C/T		P-value = 0.003 between BPD cases and controls; P-value = 0...... P-value = 0.003 between BPD cases and controls; P-value = 0.028 between all cases and controls More...	it was associated with bipolar disorder it was associated with bipolar disorder	Positive

SNP related genes (count: 2)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
HMGB1P42	high mobility group box 1 pseudogene 42	11q23.3	Mapped by Literature SNP
GRIK4	glutamate receptor, ionotropic, kainate 4	11q23.3	2(1/1/0)

SNPs in LD with rs602104 (count: 7) View in gBrowse (chr11:120938005..120953983 )

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]
rs520332	intron_variant; non_coding_transcript_variant	0.935[CEU]
rs591252	intron_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CEU]; 1.0[TSI]
rs11218078	intron_variant; non_coding_transcript_variant	0.887[CEU]; 0.804[TSI]
rs11218077	intron_variant; non_coding_transcript_variant	0.929[CEU]
rs597670	intron_variant; non_coding_transcript_variant	0.94[CEU]
rs474867	intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.943[CEU]; 0.87[TSI]
rs584092	intron_variant; non_coding_transcript_variant	0.932[CEU]

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

Reference	Statistical Result	Description	Result Category
Pickard, B. S., 2006	P-value = 0.425 between SCZ cases and controls; P-value = 0.028 between all cases and controls		Positive

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