ADHDgene Database

SNP Report

Basic Info

Name	rs2842643 dbSNP Ensembl
Location	Chr6:41650736(Fwd)
Variant Alleles	C/T
Ancestral Allele	T
Functional Annotation	downstream_gene_variant; upstream_gene_variant.
Consequence to Transcript	downstream_gene_variant(ENST00000230323; ENST00000343317; ENST00000406563; ENST00000373033; ENST00000494822; ENST00000419396; ENST00000358871; ENST00000394283; ENST00000416140; ENST00000419574; ENST00000420312; ENST00000403298) upstream_gene_variant(ENST00000597468)
No. of Studies	1 (significant: 0; non-significant: 0; trend: 1)
Source	Literature-origin

SNP related studies (count: 1)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result of Statistical Analysis
Lesch KP, 2008			ANOVA P-value=3.28E-06, Mean of ranks=70 ANOVA P-value=3.28E-06, Mean of ranks=70	one of the top 30 single SNPs located in gene regions (inclu...... one of the top 30 single SNPs located in gene regions (including 100kb of flanking sequences) ranked according to the mean rank calculated across three statistics; annotated by GWAS Catalog More...	Trend

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (significant/non-significant/trend)
TFEB	transcription factor EB	6p21	1(0/0/1)

SNPs in LD with rs2842643 (count: 8) View in gBrowse (chr6:41646885..41664727 )

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]
rs9369302	intron_variant; upstream_gene_variant	0.874[ASW]; 0.956[CEU]; 1.0[CHB]; 1.0[CHD]; 0.912[GIH]; 1.0[JPT]; 0.864[LWK]; 1.0[MEX]; 0.858[MKK]; 1.0[TSI]; 0.914[YRI]
rs1062966	downstream_gene_variant; synonymous_variant; upstream_gene_variant	1.0[ASW]; 1.0[CEU]; 1.0[CHB]; 1.0[CHD]; 1.0[GIH]; 1.0[JPT]; 0.955[MEX]; 1.0[TSI]; 0.919[YRI]
rs2842646	downstream_gene_variant	0.956[CEU]; 1.0[CHB]; 1.0[JPT]; 0.849[YRI]
rs2246159	downstream_gene_variant; upstream_gene_variant	0.842[CHB]; 1.0[JPT]; 1.0[YRI]
rs4472338	intron_variant	0.956[CEU]; 1.0[CHB]; 1.0[CHD]; 0.969[GIH]; 0.85[JPT]; 0.867[MEX]; 0.974[TSI]
rs2073157	downstream_gene_variant; intron_variant; nc_transcript_variant	1.0[CEU]; 1.0[CHB]; 0.964[CHD]; 1.0[GIH]; 1.0[JPT]; 0.955[MEX]; 1.0[TSI]
rs973361	downstream_gene_variant	0.951[CEU]; 1.0[CHB]; 1.0[JPT]; 0.848[YRI]
rs2073156	downstream_gene_variant; intron_variant; upstream_gene_variant	1.0[CEU]; 0.931[CHB]; 1.0[JPT]; 1.0[YRI]