SNP Report

Basic Info

Name	rs1060041 dbSNP Ensembl
Location	chr1:168004738 - 168004738(1)
Variant Alleles	C/T
Ancestral Allele	C
Minor Allele	T
Minor Allele Frequence	0.167931
Functional Annotation	NMD_transcript_variant; synonymous_variant.
Consequence to Transcript	NMD_transcript_variant(ENST00000470721); synonymous_variant(ENST00000312263, ENST00000367840, ENST00000367843, ENST00000432587, ENST00000470721)
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
Saito T., 2014	T/C		First-set screening: P-value_corrected=1, P-value=...... First-set screening: P-value_corrected=1, P-value=0.749, OR=1.03, 95%CI=0.85-1.25 More...	No significant association was observed. No significant association was observed.	Negative

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
DCAF6	DDB1 and CUL4 associated factor 6	1q23.3	1(0/1/0)

SNPs in LD with rs1060041 (count: 7) View in gBrowse (chr1:167917264..168049602 )

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]
rs4657727	downstream_gene_variant; intron_variant; NMD_transcript_variant; upstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs7535138	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[JPT]
rs17557162	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs2420	3_prime_UTR_variant; downstream_gene_variant; upstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs17485889	intron_variant; non_coding_transcript_variant	1.0[CHB]; 0.862[CHD]; 0.877[JPT]
rs12404574	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs11587594	intron_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[JPT]

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

Reference	Statistical Result	Description	Result Category
Saito T., 2014	First-set screening: P-value_corrected=1, P-value=0.0481, OR=1.21, 95%CI=1.00-1.46	Significant association was observed.	Positive

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