SNP Report

Basic Info

Name	rs2989476 dbSNP Ensembl
Location	chr1:60593587 - 60593587(1)
Variant Alleles	G/C
Ancestral Allele	G
Minor Allele	G
Minor Allele Frequence	0.439497
Functional Annotation	intron_variant; non_coding_transcript_variant.
Consequence to Transcript	intron_variant(ENST00000439156, ENST00000634281, ENST00000634836, ENST00000635048, ENST00000635616); non_coding_transcript_variant(ENST00000439156, ENST00000634281, ENST00000634836, ENST00000635048, ENST00000635616)
No. of Studies	3 (Positive: 0; Negative: 2; Trend: 1)
Source	Literature
Overlap with SZ?	NO
Overlap with MDD?	NO

SNP related studies (count: 3)

Reference	Allele Change	Statistical Values	Author Comments	Result Category
Smith, E. N.,2011	C/G	Genome-Wide Association: OR=1.12, P-value = 0.0299 Genome-Wide Association: OR=1.12, P-value = 0.0299	No significant association was observed. No significant association was observed.	Negative
Jiang, Y.,2011		Non-weighted test under H0: P-value(additive)=0.0000227, P-v...... Non-weighted test under H0: P-value(additive)=0.0000227, P-value(dominant)=0.0000022, P-value(recessive)=0.0461; weighted test under H'0: P-value(additive)=0.0000266, P-value(dominant)=0.00000225, P-value(recessive)=0.0727; logistic regression: P-value(additive)=0.0000403, P-value(dominant)=0.00000323, P-value(recessive)=0.0606 More...	Suggestive association was found. Suggestive association was found.	Trend
Ollila, H. M.,2009	G/C	FBAT: P-value = 0.892598 FBAT: P-value = 0.892598	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)
NFIA	nuclear factor I/A	1p31.3-p31.2	1(0/1/0)

SNPs in LD with rs2989476 (count: 22) View in gBrowse (chr1:60541510..60653259 )

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: 22)

rs_ID	Functional Annotation	r²[population]
rs552294	intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.959[CEU]; 0.89[TSI]
rs12094280	intron_variant; non_coding_transcript_variant	0.842[CEU]
rs898729	intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CEU]
rs1461359	intron_variant; non_coding_transcript_variant	0.88[CEU]
rs1381168	intron_variant; non_coding_transcript_variant	0.842[CEU]
rs4259696	intron_variant; non_coding_transcript_variant	0.805[CEU]
rs10889189	intron_variant; non_coding_transcript_variant	0.908[TSI]
rs10218679	intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.92[CEU]; 0.89[TSI]
rs10889187	intron_variant; non_coding_transcript_variant	0.805[CEU]; 0.805[TSI]
rs1572358	intron_variant; non_coding_transcript_variant	0.842[CEU]; 0.825[TSI]
rs484743	intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.92[CEU]; 0.89[TSI]
rs7522761	intron_variant; non_coding_transcript_variant	0.835[CEU]
rs10889191	intron_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CEU]; 0.977[TSI]
rs528598	intron_variant; non_coding_transcript_variant	0.883[CEU]; 0.849[TSI]
rs1381171	intron_variant; non_coding_transcript_variant	0.876[CEU]; 0.825[TSI]
rs11207633	intron_variant; non_coding_transcript_variant	0.805[CEU]; 0.805[TSI]
rs10889186	intron_variant; non_coding_transcript_variant	0.805[CEU]
rs2989477	intron_variant; non_coding_transcript_variant	0.815[CEU]
rs6661702	intron_variant; non_coding_transcript_variant	0.919[CEU]
rs1841565	intron_variant; non_coding_transcript_variant	0.815[CEU]
rs2363079	non_coding_transcript_exon_variant; non_coding_transcript_variant	0.874[CEU]
rs564367		0.82[TSI]

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

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