SNP Report

Basic Info

Name	rs4792938 dbSNP Ensembl
Location	chr17:44347231 - 44347231(1)
Variant Alleles	G/C
Ancestral Allele	C
Minor Allele	G
Minor Allele Frequence	0.377396
Functional Annotation	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant.
Consequence to Transcript	intron_variant(ENST00000053867, ENST00000585512, ENST00000586782, ENST00000587109, ENST00000587387, ENST00000587518, ENST00000587958, ENST00000588143, ENST00000588170, ENST00000588237, ENST00000589265, ENST00000589536, ENST00000591740, ENST00000592323, ENST00000592783, ENST00000593167, LRG_661t1); NMD_transcript_variant(ENST00000586782); non_coding_transcript_variant(ENST00000587958, ENST00000588170, ENST00000592323); upstream_gene_variant(ENST00000585348, ENST00000586242, ENST00000586443, ENST00000589923, ENST00000590984)
No. of Studies	2 (Positive: 1; Negative: 1; Trend: 0)
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
Galimberti, D., 2014	G/C		P > 0.05 P > 0.05	In contrast to data obtained in that previous study, as rega...... In contrast to data obtained in that previous study, as regards rs4792938, we did not observe an association in our population. More...	Negative
Galimberti, D.,2012	G/C		Association analysis: chi square test, genotype P-value = 0...... Association analysis: chi square test, genotype P-value = 0.0003, OR: 0.37, 95%CI: 0.22-0.63; allele P-value = 0.01, OR: 0.66, 95%CI: 0.49-0.90. More...	Significant association was observed in BD. Significant association was observed in BD.	Positive

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
GRN	granulin	17q21.32	2(2/0/0)

SNPs in LD with rs4792938 (count: 3) View in gBrowse (chr17:44336113..44347231 )

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]
rs3859268	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.877[CEU]
rs3760365	upstream_gene_variant	0.877[CEU]
rs7216307	downstream_gene_variant	0.958[CEU]

Overlap with SZ from cross-disorder studies (count: 2)

Reference	Statistical Result	Description	Result Category
Galimberti, D., 2014		Tagging single nucleotide polymorphisms (SNPs) rs2879096 and rs4792938, along with rs5848, previously shown to be associated with BD and schizophrenia	Positive
Galimberti, D.,2012	Association analysis:chi square test, genotype P-value = 0.002, OR: 0.48, 95%CI: 0.31-0.77;allele P-value > 0.05	Significant association was observed in SZ.	Positive

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