SNP Report

Basic Info

Name	rs879606 dbSNP Ensembl
Location	chr17:39625596 - 39625596(1)
Variant Alleles	A/G
Ancestral Allele	G
Minor Allele	A
Minor Allele Frequence	0.362021
Functional Annotation	downstream_gene_variant; upstream_gene_variant.
Consequence to Transcript	downstream_gene_variant(ENST00000398554); upstream_gene_variant(ENST00000254079, ENST00000394265, ENST00000394267, ENST00000492037, ENST00000579000, ENST00000580772, ENST00000580825, ENST00000582680, ENST00000583446)
No. of Studies	1 (Positive: 0; Negative: 1; Trend: 0)
Source	Literature
Overlap with SZ?	YES
Overlap with MDD?	NO

SNP related studies (count: 1)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Yoshimi, A., 2008	G/A	A	Genotypic P-value = 0.857, Armitage's P-value = 0.580. allel...... Genotypic P-value = 0.857, Armitage's P-value = 0.580. allelic P-value = 0.306 in BD. More...		Negative

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
PPP1R1B	protein phosphatase 1, regulatory (inhibitor) subunit 1B	17q12	1(0/1/0)

SNPs in LD with rs879606 (count: 37) View in gBrowse (chr17:39589726..39683240 )

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: 37)

rs_ID	Functional Annotation	r²[population]
rs11078919	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.822[JPT]
rs8078228	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.812[JPT]
rs12150603	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.822[JPT]
rs1874228	upstream_gene_variant	0.954[CHB]; 1.0[CHD]; 1.0[JPT]
rs903501	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.822[JPT]
rs9972882	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.868[CHB]; 0.832[CHD]; 0.822[JPT]
rs1053651	downstream_gene_variant; synonymous_variant; upstream_gene_variant	0.868[CHB]; 0.832[CHD]; 0.822[JPT]
rs14050	3_prime_UTR_variant; downstream_gene_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	0.822[JPT]
rs881844	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.829[CHB]; 0.822[JPT]
rs2941505	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.822[JPT]
rs2271308	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.829[CHB]; 0.81[CHD]; 0.822[JPT]
rs2517957	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.894[JPT]
rs12940986	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.822[JPT]
rs931992	5_prime_UTR_variant; downstream_gene_variant; upstream_gene_variant	0.829[CHB]; 0.81[CHD]; 0.822[JPT]
rs2952151	3_prime_UTR_variant; downstream_gene_variant; missense_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	0.822[JPT]
rs11869286	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.868[CHB]; 0.832[CHD]; 0.816[JPT]
rs903502	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.822[JPT]
rs2271309	intron_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs12150298	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.822[JPT]
rs1565922	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.816[JPT]
rs1476278	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.822[JPT]
rs9915323	upstream_gene_variant	0.907[CHB]; 0.855[JPT]
rs2941504	3_prime_UTR_variant; 5_prime_UTR_variant; downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; synonymous_variant	0.822[JPT]
rs907087	3_prime_UTR_variant; downstream_gene_variant; missense_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	0.822[JPT]
rs9303274	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.822[JPT]
rs2517958	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.81[JPT]
rs12453682	upstream_gene_variant	0.82[CHB]; 0.875[CHD]; 0.847[JPT]
rs9675194	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.822[JPT]
rs907089	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.822[JPT]
rs2941503	3_prime_UTR_variant; downstream_gene_variant; missense_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	0.819[JPT]
rs2313171	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.806[JPT]
rs1877031	downstream_gene_variant; missense_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.868[CHB]; 0.832[CHD]; 0.822[JPT]
rs10852934	downstream_gene_variant; upstream_gene_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs11654954		0.822[CHD]
rs2934953	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.85[JPT]
rs2247862	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.822[JPT]
rs4795388	upstream_gene_variant	0.954[CHB]; 0.952[CHD]; 0.951[JPT]

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

Reference	Statistical Result	Description	Result Category
Yoshimi, A., 2008	Genotypic P-value = 0.631, Armitage's P-value = 0.985. allelic P-value = 0.985 in SZ.	Single-marker in a sample set showed that PPP1R1B polymorphisms were not significantly associated with schizophrenia.	Negative

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