SNP Report

Basic Info

Name	rs2759346 dbSNP Ensembl
Location	chr1:231813075 - 231813075(1)
Variant Alleles	A/G
Ancestral Allele	A
Minor Allele	A
Minor Allele Frequence	0.492612
Functional Annotation	intron_variant; NMD_transcript_variant; upstream_gene_variant.
Consequence to Transcript	intron_variant(ENST00000295051, ENST00000366632, ENST00000366633, ENST00000366636, ENST00000366637, ENST00000422590, ENST00000439617, ENST00000535944, ENST00000535983, ENST00000537876, ENST00000539444, ENST00000602281, ENST00000602567, ENST00000602634, ENST00000602700, ENST00000602713, ENST00000602822, ENST00000602873, ENST00000602885, ENST00000602956, ENST00000602962, ENST00000620189, ENST00000622252, ENST00000628350); NMD_transcript_variant(ENST00000295051, ENST00000366632, ENST00000422590, ENST00000535944, ENST00000602567, ENST00000602634, ENST00000602700, ENST00000602713, ENST00000602822, ENST00000602885, ENST00000602956, ENST00000602962); upstream_gene_variant(ENST00000612827)
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
Thomson, P. A.,2005(a)			Single-Marker Analysis: allele frequency, for BP, P-value = ...... Single-Marker Analysis: allele frequency, for BP, P-value = 0.69 More...	No significant association was observed. No significant association was observed.	Negative
Perlis, 2008			Mean X²=4.43, P-value = 0.01 in gene-based associ...... Mean X²=4.43, P-value = 0.01 in gene-based association tests More...		Positive

SNP related genes (count: 2)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
TSNAX	translin-associated factor X	1q42.2	4(3/1/0)
DISC1	disrupted in schizophrenia 1	1q42.1	18(10/7/1)

SNPs in LD with rs2759346 (count: 2) View in gBrowse (chr1:231813075..231831116 )

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]
rs6674099		intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.841[TSI]
rs1535530		3_prime_UTR_variant; downstream_gene_variant; intron_variant; NMD_transcript_variant; upstream_gene_variant	0.868[CEU]

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

Reference	Statistical Result	Description	Result Category
Thomson, P. A.,2005(a)	Single-Marker Analysis:allele frequency, for SZ, P-value = 0.83	No significant association was observed.	Negative

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