SNP Report

Basic Info

Name	rs1630250 dbSNP Ensembl
Location	chr1:231528457 - 231528457(1)
Variant Alleles	G/C
Ancestral Allele	C
Minor Allele	G
Minor Allele Frequence	0.45647
Functional Annotation	non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant.
Consequence to Transcript	non_coding_transcript_exon_variant(ENST00000416221, ENST00000425412, ENST00000454631); non_coding_transcript_variant(ENST00000416221, ENST00000425412, ENST00000454631); upstream_gene_variant(ENST00000366639, ENST00000413309, ENST00000440665, ENST00000450783, ENST00000476913, ENST00000602567, ENST00000602634, ENST00000602825, ENST00000602885, ENST00000602956, ENST00000602962)
No. of Studies	3 (Positive: 0; Negative: 3; Trend: 0)
Source	Literature
Overlap with SZ?	YES
Overlap with MDD?	YES

SNP related studies (count: 3)

Reference	Allele Change	Statistical Values	Author Comments	Result Category
Palo, O. M., 2007	G/C	P-value = 0.632 in all patients, P-value = 0.572 in males, P...... P-value = 0.632 in all patients, P-value = 0.572 in males, P-value = 0.104 in females, with bipolar spectrum disorder More...		Negative
Okuda, A.,2010	C/G	chi square test: genotype P-value = 0.493, allele P-value = ...... chi square test: genotype P-value = 0.493, allele P-value = 0.892 More...	No significant association was observed in BD. No significant association was observed in BD.	Negative
Thomson, P. A.,2005(a)		Single-Marker Analysis: allele frequency, for BP, P-value = ...... Single-Marker Analysis: allele frequency, for BP, P-value = 0.79 More...	No significant association was observed. No significant association was observed.	Negative

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 rs1630250 (count: 39) View in gBrowse (chr1:231430873..231594375 )

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: 39)

rs_ID	Functional Annotation	r²[population]
rs1769795		0.867[CHB]; 0.952[JPT]
rs1769802		0.955[CHB]; 0.912[JPT]
rs1416910	downstream_gene_variant	0.909[CHB]
rs961154		0.953[CHB]; 0.952[JPT]
rs1765780		0.953[CHB]; 0.952[JPT]
rs1655290	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.827[CHB]
rs7533573	intron_variant; NMD_transcript_variant	0.959[CEU]
rs16854388	downstream_gene_variant	0.827[CHB]
rs1769801		0.955[CHB]; 0.955[JPT]
rs1612154	downstream_gene_variant; intron_variant; NMD_transcript_variant	0.836[CEU]
rs1765791	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.847[CEU]
rs1769810		0.913[CHB]; 0.864[JPT]
rs1619386	intron_variant; NMD_transcript_variant	0.842[CEU]
rs1416909	downstream_gene_variant	0.834[CHB]
rs3125933	downstream_gene_variant; intron_variant; NMD_transcript_variant	0.854[CEU]
rs1416908	downstream_gene_variant	0.83[CHB]
rs1765797		0.953[CHB]; 0.952[JPT]
rs1765787		0.953[CHB]; 0.952[JPT]
rs12040246	downstream_gene_variant; intron_variant; NMD_transcript_variant	0.862[JPT]
rs1655293		0.865[CHB]
rs2808579	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CEU]; 1.0[CHB]; 0.952[JPT]
rs2790859		0.953[CHB]; 0.952[JPT]
rs1982095	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.961[CEU]
rs1655281		0.955[CHB]; 0.955[JPT]
rs1765814		0.955[CHB]; 0.955[JPT]
rs16854395	downstream_gene_variant	0.87[CHB]
rs1765794	downstream_gene_variant	0.813[CEU]; 0.953[CHB]; 1.0[JPT]
rs1765782	intron_variant; NMD_transcript_variant	0.959[CEU]
rs1765805		0.904[JPT]
rs1769798	downstream_gene_variant	0.955[CHB]; 0.955[JPT]
rs1769800		1.0[CHB]; 0.955[JPT]
rs1655288	intron_variant; NMD_transcript_variant	0.856[CEU]
rs1769794		0.955[CHB]; 0.955[JPT]
rs1621135	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.834[CHB]
rs1765798		0.861[CHB]; 0.951[JPT]
rs1765785		0.953[CHB]; 0.951[JPT]
rs2790860	downstream_gene_variant	0.952[CHB]; 0.952[JPT]
rs12093061		0.905[CHB]; 0.952[JPT]
rs1655305	intron_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	0.842[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 = 0.95	No significant association was observed.	Negative

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

Reference	Statistical Result	Description	Result Category
Okuda, A.,2010	chi square test:genotype P-value = 0.356, allele P-value = 0.165	No significant association was observed.	Negative