SNP Report

Basic Info

Name	rs3117099 dbSNP Ensembl
Location	chrCHR_HSCHR6_MHC_SSTO_CTG1:32397879 - 32397879(1)
Variant Alleles	G/A
Ancestral Allele	G
Minor Allele	A
Minor Allele Frequence	0.317692
Functional Annotation	downstream_gene_variant; upstream_gene_variant; intron_variant.
Consequence to Transcript	downstream_gene_variant(ENST00000374993, ENST00000454136, ENST00000465865, ENST00000544175); upstream_gene_variant(ENST00000426643); intron_variant(ENST00000613328, ENST00000445928, ENST00000452747, ENST00000549560, ENST00000550327, ENST00000433741, ENST00000416597, ENST00000418649, ENST00000549943, ENST00000552479, ENST00000416528, ENST00000447918, ENST00000457589, ENST00000548832, ENST00000551095, ENST00000553032, ENST00000445536, ENST00000416387, ENST00000451625, ENST00000548717, ENST00000551409, ENST00000551686, ENST00000416228, ENST00000435335, ENST00000443091, ENST00000549852, ENST00000551471, ENST00000412919, ENST00000422056, ENST00000550531, ENST00000550698, ENST00000444345, ENST00000427760, ENST00000433826, ENST00000548253, ENST00000548835, ENST00000551669, ENST00000428633)
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
Bergen, S. E.,2012		A	logistic regression: P-value > E-05 logistic regression: P-value > E-05	No significant association was observed in BD. No significant association was observed in BD.	Negative

SNP related genes (count: 2)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
HCG23	HLA complex group 23 (non-protein coding)	6p21	Mapped by Literature SNP
BTNL2	butyrophilin-like 2	6p21.3	Mapped by Literature SNP

SNPs in LD with rs3117099 (count: 2) View in gBrowse (chrCHR_HSCHR6_MHC_SSTO_CTG1:32380509..32397879 )

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

rs_ID	Literature-origin SNPs with LD	Functional Annotation	r²[population]
rs3129945		upstream_gene_variant	1.0[CEU]
rs3129944		upstream_gene_variant	1.0[CEU]

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

Reference	Statistical Result	Description	Result Category
Bergen, S. E.,2012	logistic regression:for SZ full sample, OR=0.79, P-value = 4.12E-06	No significant association was observed in SZ.	Negative

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