SNP Report

Basic Info

Name	rs406511 dbSNP Ensembl
Location	chrCHR_HSCHR6_MHC_SSTO_CTG1:29409086 - 29409086(1)
Variant Alleles	C/G
Ancestral Allele	C
Minor Allele	G
Minor Allele Frequence	0.0283546
Functional Annotation	intron_variant; upstream_gene_variant.
Consequence to Transcript	intron_variant(ENST00000377154, ENST00000446761, ENST00000508665); upstream_gene_variant(ENST00000441440, ENST00000505384, ENST00000430148, ENST00000444009, ENST00000458372, ENST00000421859, ENST00000502578, ENST00000418692)
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		C	logistic regression: OR=1.41, P-value = 9.07E-06 logistic regression: OR=1.41, P-value = 9.07E-06	No significant association was observed in BD. No significant association was observed in BD.	Negative

SNP related genes (count: 0)

SNPs in LD with rs406511 (count: 30) View in gBrowse (chrCHR_HSCHR6_MHC_SSTO_CTG1:29373556..29591380 )

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: 30)

rs_ID	Functional Annotation	r²[population]
rs9257803	intron_variant; upstream_gene_variant	0.831[CEU]
rs926552	downstream_gene_variant; intron_variant; upstream_gene_variant	0.847[CEU]
rs429479	intron_variant	1.0[CEU]; 1.0[TSI]
rs1233491	upstream_gene_variant	1.0[CEU]; 0.884[TSI]
rs2523431		1.0[CEU]
rs1233393	downstream_gene_variant; intron_variant; upstream_gene_variant	0.847[CEU]
rs9257805	intron_variant; upstream_gene_variant	0.831[CEU]
rs1233494	downstream_gene_variant	1.0[CEU]
rs2523443	intron_variant; upstream_gene_variant; non_coding_transcript_variant	1.0[CEU]; 0.884[TSI]
rs1233385	downstream_gene_variant; intron_variant	0.847[CEU]
rs9257809	intron_variant	1.0[CEU]; 1.0[TSI]
rs1233480	intron_variant; non_coding_transcript_variant	1.0[CEU]
rs2523432		1.0[CEU]
rs2746150	downstream_gene_variant	1.0[CEU]; 0.884[TSI]
rs1235162	intron_variant; upstream_gene_variant	0.831[CEU]; 0.884[TSI]
rs9257800	downstream_gene_variant; intron_variant	0.831[CEU]
rs1233396	downstream_gene_variant; intron_variant; upstream_gene_variant	0.847[CEU]
rs442694	intron_variant	1.0[CEU]; 0.884[TSI]
rs2143668	downstream_gene_variant	1.0[CEU]
rs2206853	downstream_gene_variant; intron_variant; non_coding_transcript_variant	1.0[CEU]
rs1535039	downstream_gene_variant; intron_variant	1.0[CEU]; 0.884[TSI]
rs1233493	upstream_gene_variant	1.0[CEU]; 0.884[TSI]
rs408623	downstream_gene_variant; upstream_gene_variant	1.0[CEU]
rs389419	downstream_gene_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	1.0[CEU]
rs404240	3_prime_UTR_variant; downstream_gene_variant; synonymous_variant	1.0[CEU]; 0.884[TSI]
rs3749971	intron_variant; missense_variant	0.831[CEU]
rs1233489	upstream_gene_variant	1.0[CEU]
rs1234844	downstream_gene_variant	1.0[CEU]
rs413670	downstream_gene_variant; intron_variant	1.0[CEU]
rs2746149	downstream_gene_variant; intron_variant; non_coding_transcript_variant	1.0[CEU]; 0.884[TSI]

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

Reference	Statistical Result	Description	Result Category
Bergen, S. E.,2012	logistic regression:P-value > E-05	No significant association was observed in SZ.	Negative

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