SNP Report

Basic Info

Name	rs8647 dbSNP Ensembl
Location	chr19:49933723 - 49933723(1)
Variant Alleles	G/A
Ancestral Allele	G
Minor Allele	A
Minor Allele Frequence	0.282548
Functional Annotation	3_prime_UTR_variant; downstream_gene_variant; intron_variant; NMD_transcript_variant; upstream_gene_variant.
Consequence to Transcript	3_prime_UTR_variant(ENST00000423777); downstream_gene_variant(ENST00000578027, ENST00000595125, ENST00000596658, ENST00000597227, ENST00000600336); intron_variant(ENST00000451973); NMD_transcript_variant(ENST00000451973); upstream_gene_variant(ENST00000341114, ENST00000352066, ENST00000422090, ENST00000593652, ENST00000594673, ENST00000595463, ENST00000595948, ENST00000596011, ENST00000596022, ENST00000596217, ENST00000596437, ENST00000596680, ENST00000597029, ENST00000597295, ENST00000597723, ENST00000597814, ENST00000598301, ENST00000599186, ENST00000599560, ENST00000599567, ENST00000599788, ENST00000599830, ENST00000600583, ENST00000600935, ENST00000601665, ENST00000601717)
No. of Studies	1 (Positive: 0; Negative: 1; 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
Kakiuchi, C., 2007 (b)	A/G		Fisher's exact test, genotypic P-value = 0.261, allelic P-va...... Fisher's exact test, genotypic P-value = 0.261, allelic P-value = 0.35 in MDMD samples, Fisher's exact test, genotypic P-value = 0.705, allelic P-value = 0.92 in MPS samples, Fisher's exact test, genotypic P-value = 0.253, allelic P-value = 0.517 in total samples; TDT P-value = 0.889, X²=0.02 in NIMH trios More...	There were no significant differences in both genotype and a...... There were no significant differences in both genotype and allele frequencies in both of total samples and independently collected age-matched samples. TDT analysis also showed no association of the SNP to the illness. More...	Negative

SNP related genes (count: 3)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
IL4I1	interleukin 4 induced 1	19q13.3-q13.4	Mapped by Literature SNP
NUP62	nucleoporin 62kDa	19q13.33	Mapped by Literature SNP
ATF5	activating transcription factor 5	19q13.33	1(0/1/0)

SNPs in LD with rs8647 (count: 9) View in gBrowse (chr19:49907293..49940804 )

The LD data used here is based on HapMap rel#27. LD SNP pairs were selected with a threshold r²<=0.8.

rs_ID	Functional Annotation	r²[population]
rs7247653	downstream_gene_variant; intron_variant; NMD_transcript_variant; upstream_gene_variant	0.881[CEU]; 0.904[JPT]
rs9523	3_prime_UTR_variant; downstream_gene_variant; intron_variant; NMD_transcript_variant	0.802[TSI]; 0.856[JPT]
rs8108252	intron_variant; NMD_transcript_variant	0.815[CEU]; 0.955[CHB]; 1.0[CHD]; 1.0[JPT]
rs8429	3_prime_UTR_variant; downstream_gene_variant; intron_variant; NMD_transcript_variant	0.802[TSI]; 0.856[JPT]
rs12610975	downstream_gene_variant; intron_variant; NMD_transcript_variant	0.859[CEU]; 1.0[CHB]; 1.0[JPT]
rs3826777	5_prime_UTR_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.848[TSI]; 0.856[JPT]
rs1044167	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.856[JPT]
rs3170545	3_prime_UTR_variant; downstream_gene_variant; intron_variant; NMD_transcript_variant; upstream_gene_variant	1.0[CEU]; 1.0[TSI]; 1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs7246342	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.847[TSI]; 0.856[JPT]

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

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