SNP Report

Basic Info

Name	rs2290279 dbSNP Ensembl
Location	chr18:10526190 - 10526190(1)
Variant Alleles	A/G
Ancestral Allele	G
Minor Allele	G
Minor Allele Frequence	0.346046
Functional Annotation	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant.
Consequence to Transcript	intron_variant(ENST00000322897, ENST00000580224, ENST00000580483, ENST00000580746, ENST00000582978); NMD_transcript_variant(ENST00000580224, ENST00000580483); non_coding_transcript_variant(ENST00000580746, ENST00000582978); upstream_gene_variant(ENST00000582472)
No. of Studies	3 (Positive: 2; Negative: 1; Trend: 0)
Source	Literature
Overlap with SZ?	NO
Overlap with MDD?	NO

SNP related studies (count: 3)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Yosifova, A.,2009	A/G		Allelic association: P-value = 0.29 Allelic association: P-value = 0.29	No significant association was observed No significant association was observed	Negative
Weller, A. E., 2006	G/A		genotypic P-value = 0.027, allelic P-value = 0.157 genotypic P-value = 0.027, allelic P-value = 0.157	showed a nominal, statistically significant association with...... showed a nominal, statistically significant association with BPD at the genotype frequency level but not at the allele frequency level More...	Positive
Li, X.,2009	G/A	G	1.BD patients and control: Allele distribution: Permutated P...... 1.BD patients and control: Allele distribution: Permutated P-value = 0.0042, Genotype distribution: P-value = 0.0028; 2.BD-I patients and control: Allele distribution: Permutated P-value = 0.003, Genotype distribution: P-value = 0.0008 More...	Significant association was observed both in the BD group an...... Significant association was observed both in the BD group and the BD-I group. More...	Positive

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
NAPG	N-ethylmaleimide-sensitive factor attachment protein, gamma	18p11.21	3(2/1/0)

SNPs in LD with rs2290279 (count: 26) View in gBrowse (chr18:10493080..10556839 )

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: 26)

rs_ID	Functional Annotation	r²[population]
rs571229	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.84[CEU]; 1.0[JPT]
rs473877		1.0[CEU]; 1.0[CHB]; 1.0[JPT]
rs11080425	downstream_gene_variant	0.824[TSI]; 0.832[CHD]
rs542448	downstream_gene_variant	0.837[CEU]; 0.9[CHB]; 0.953[JPT]
rs665604	downstream_gene_variant	0.867[CEU]; 0.866[CHB]; 0.953[JPT]
rs520666		0.824[TSI]; 0.909[CHB]; 1.0[CHD]; 0.909[JPT]
rs540701	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.84[CEU]; 1.0[JPT]
rs526394	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.84[CEU]; 0.953[JPT]
rs547010	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.833[CEU]; 0.862[CHB]; 0.877[CHD]; 0.951[JPT]
rs485954	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.84[CEU]; 1.0[CHB]; 1.0[JPT]
rs510558	downstream_gene_variant	0.837[CEU]; 0.953[CHB]; 1.0[JPT]
rs16974630		0.807[CHD]
rs551586	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.84[CEU]; 0.802[CHD]; 0.953[JPT]
rs571279	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.867[CEU]; 1.0[JPT]
rs580216	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.84[CEU]; 0.829[CHB]; 0.862[CHD]; 1.0[JPT]
rs616139	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.84[CEU]; 0.954[CHB]; 1.0[JPT]
rs10207	3_prime_UTR_variant; downstream_gene_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	0.84[CEU]; 0.952[CHB]; 1.0[JPT]
rs632245	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.84[CEU]; 0.954[CHB]; 0.975[CHD]; 1.0[JPT]
rs512710	upstream_gene_variant	1.0[CEU]; 0.977[TSI]; 1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs568689		0.822[CHB]; 1.0[JPT]
rs2197166	downstream_gene_variant	0.824[TSI]; 0.832[CHD]
rs588608	upstream_gene_variant	1.0[CEU]; 1.0[CHB]; 0.952[JPT]
rs9676242	downstream_gene_variant	0.84[CEU]; 0.954[CHB]; 1.0[JPT]
rs533675	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.837[CEU]; 0.95[JPT]
rs546966	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.84[CEU]; 0.829[CHB]; 0.86[CHD]; 1.0[JPT]
rs11873815		1.0[CHB]; 1.0[JPT]

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

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