SNP Report

Basic Info

Name	rs7872515 dbSNP Ensembl
Location	chr9:92060258 - 92060258(1)
Variant Alleles	G/A
Ancestral Allele	A
Minor Allele	A
Minor Allele Frequence	0.303514
Functional Annotation	intron_variant; non_coding_transcript_variant.
Consequence to Transcript	intron_variant(ENST00000262554, ENST00000482632, LRG_272t1); non_coding_transcript_variant(ENST00000482632)
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)
RORA	RAR-related orphan receptor A	15q21-q22	3(2/1/0)
SPTLC1	serine palmitoyltransferase, long chain base subunit 1	9q22.31	1(0/1/0)

SNPs in LD with rs7872515 (count: 15) View in gBrowse (chr9:91948734..92115554 )

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]
rs7856177	downstream_gene_variant; intron_variant; non_coding_transcript_variant	1.0[CEU]
rs7852067	intron_variant	1.0[CEU]
rs7860518	intron_variant; non_coding_transcript_variant	0.899[CEU]
rs6479397	downstream_gene_variant	0.827[TSI]
rs1970121	downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CEU]
rs10123181	downstream_gene_variant	0.883[TSI]
rs7858659	intron_variant; non_coding_transcript_variant	0.815[CEU]
rs7029539	intron_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CEU]
rs10992221	intron_variant; non_coding_transcript_variant	1.0[CEU]; 1.0[TSI]
rs10820936	intron_variant; non_coding_transcript_variant	0.815[CEU]
rs10820937	downstream_gene_variant; intron_variant; non_coding_transcript_variant	1.0[CEU]
rs10992234	downstream_gene_variant; upstream_gene_variant	1.0[CEU]
rs3750440	5_prime_UTR_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.89[CEU]
rs7872238	downstream_gene_variant	0.883[TSI]
rs16908106	intron_variant; non_coding_transcript_variant	0.883[TSI]

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=0.73, P-value = 6.65E-06	No significant association was observed in SZ.	Negative

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