SNP Report

Basic Info

Name	rs7839852 dbSNP Ensembl
Location	chr8:28848548 - 28848548(1)
Variant Alleles	T/C
Ancestral Allele	T
Minor Allele	C
Minor Allele Frequence	0.234425
Functional Annotation	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant.
Consequence to Transcript	downstream_gene_variant(ENST00000520831); intron_variant(ENST00000416984, ENST00000518510, ENST00000520184, ENST00000520437, ENST00000520983, ENST00000521022, ENST00000521777, ENST00000522363, ENST00000523303, ENST00000523436, ENST00000524081); NMD_transcript_variant(ENST00000518510, ENST00000520437, ENST00000522363, ENST00000523303); non_coding_transcript_variant(ENST00000520983)
No. of Studies	1 (Positive: 1; Negative: 0; Trend: 0)
Source	Literature
Overlap with SZ?	NO
Overlap with MDD?	NO

SNP related studies (count: 1)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Hattori, E.,2009			In GWAS: Allelic P-value = 0.03331, Genotypic P-value = 0.00...... In GWAS: Allelic P-value = 0.03331, Genotypic P-value = 0.00979, Recessive P-value = 0.0041, HWE P-value = 0.17537; in Follow-up study: MAF=0.45, Allelic P-value = 0.00512, Allelic Q-value=0.49274, HWE P-value = 0.23017 More...	Significant association was observed in both GWAS and Follow...... Significant association was observed in both GWAS and Follow-up study. More...	Positive

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
INTS9	integrator complex subunit 9	8p21.1	1(1/0/0)

SNPs in LD with rs7839852 (count: 21) View in gBrowse (chr8:28782853..28854394 )

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: 21)

rs_ID	Functional Annotation	r²[population]
rs17059413	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CHB]; 0.901[CHD]; 0.867[JPT]
rs6558079	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CHB]; 0.949[CHD]; 0.909[JPT]
rs17059456	intron_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CHB]; 0.975[CHD]; 0.951[JPT]
rs6998570	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CHB]; 0.975[CHD]; 0.953[JPT]
rs6558080	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CHB]; 0.953[JPT]
rs7814699	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CHB]; 0.949[CHD]; 0.909[JPT]
rs241188	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.829[CHB]
rs241189	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.829[CHB]
rs3824092	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CHB]; 0.975[CHD]; 0.953[JPT]
rs17059506	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.954[CHB]; 0.909[JPT]
rs7841719	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CHB]; 0.953[JPT]
rs17059487	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CHB]; 0.95[CHD]; 0.953[JPT]
rs6997949	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CHB]; 0.953[JPT]
rs3735724	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CHB]; 0.95[CHD]; 1.0[JPT]
rs13258975	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CHB]; 0.904[JPT]
rs7843943	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CHB]; 0.975[CHD]; 0.953[JPT]
rs7830064	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CHB]; 0.953[JPT]
rs1005253	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CHB]; 0.953[JPT]
rs11998357	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CHB]; 0.952[JPT]
rs3802155	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CHB]; 0.953[JPT]
rs11984552	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CHB]; 0.846[JPT]

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

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