SNP Report

Basic Info

Name	rs1800629 dbSNP Ensembl
Location	chrCHR_HSCHR6_MHC_SSTO_CTG1:31565999 - 31565999(1)
Variant Alleles	G/A
Ancestral Allele	G
Minor Allele	A
Minor Allele Frequence	0.0902556
Functional Annotation	downstream_gene_variant; upstream_gene_variant.
Consequence to Transcript	downstream_gene_variant(ENST00000418386, ENST00000454783, ENST00000471842, ENST00000489638); upstream_gene_variant(ENST00000449264, ENST00000383303, ENST00000383304, ENST00000476761, ENST00000490708, ENST00000376122, ENST00000432632, ENST00000441939, ENST00000464821, ENST00000487391, ENST00000420425, ENST00000436519, ENST00000454550, ENST00000461499, ENST00000479906, ENST00000412275, ENST00000448630, ENST00000456789, ENST00000466460, ENST00000468015, ENST00000448781, ENST00000383499, ENST00000400272, ENST00000481446, ENST00000498217, ENST00000383496, ENST00000412851, ENST00000426845, ENST00000464086, ENST00000473355, ENST00000443707)
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
Yosifova, A.,2009	A/G		Allelic association: P-value = 0.79 Allelic association: P-value = 0.79	No significant association was observed No significant association was observed	Negative
Czerski, P. M., 2008		G	The frequency of the TNF -308G allele was 86.8% in BPAD pati...... The frequency of the TNF -308G allele was 86.8% in BPAD patients and 82.9% in control subjects, which was statistically significant (p = 0.039). The frequency of the TNF -308G/G genotype was not significantly (p = 0.070) but trend-like different in patients versus controls (74.8 vs. 68.9%). More...	We observed an association of the -308G allele with both SCH...... We observed an association of the -308G allele with both SCH and BPAD, and also with a positive family history in patients with SCH and BPAD. More...	Positive

SNP related genes (count: 2)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
LTA	lymphotoxin alpha	6p21.3	Mapped by Literature SNP
TNF	tumor necrosis factor	6p21.3	4(2/2/0)

SNPs in LD with rs1800629 (count: 4) View in gBrowse (chrCHR_HSCHR6_MHC_SSTO_CTG1:31515424..31591433 )

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]
rs3093975	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.893[CEU]
rs2857595		0.841[CEU]
rs3093988	upstream_gene_variant	0.894[CEU]; 0.871[TSI]
rs2516482	5_prime_UTR_variant; downstream_gene_variant	1.0[CEU]; 1.0[TSI]

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

Reference	Statistical Result	Description	Result Category
Czerski, P. M., 2008	The frequency of the TNF -308G allele was 87.9% in SCH patients and 82.9% in control subjects, which was statistically significant (p = 0.008). The frequency of the TNF -308G/G genotype was significantly (p = 0.018) higher in patients than in controls (76.7 vs. 68.9%).	Our results may point to an association of the TNF -308G allele and -308G/G genotype with both SCH and BPAD, and to a relationship of the -308G allele with the risk of SCH and BPAD in patients with a positive family history. TNF could be potentially a susceptibility gene, shared between SCH and BPAD.	Positive

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