Combination of tag SNP alleles defining each haplotype and frequencies

<p>Haplotype tagging SNPs are indicated in bold. (0) indicates the allele with major frequency, (1) the allele with minor frequency.</p

PIk3R1 SNPs: position and minor allele frequencies

<p>PIk3R1 SNPs: position and minor allele frequencies</p

UCSC genome browser generated view of genomic region of <i>PIK3R1</i> including exons 2 to 7.

<p>Coding exons are represented by blocks connected by horizontal lines representing introns. The 5′ untranslated regions (UTRs) are displayed as thinner blocks on the leading ends of the aligning regions. Arrowheads on the connecting intron lines indicate the direction of transcription. Position of CpG islands, putative promoter and transcription start sites are indicated. Location of transcription factor binding sites conserved in the human/mouse/rat alignment is indicated. Conservation of binding sites in all 3 species is computed with the Transfac Matrix Database (v7.0). Evolutionary conservation in 17 vertebrates, including mammalian, amphibian, bird, and fish species was scored by the phastCons program following MULTIZ alignments. Conservation scores are displayed as wiggle, where the height reflects the size of the score. Pairwise alignments of each species to the human genome are displayed below as a “wiggle” that indicates alignment quality.</p

Association of <i>PIK3R1</i> SNPs with alcohol consumption patterns in adolescents (TDT)

<p>T = transmitted, U untransmitted</p>a<p>Subject has never been drunk vs. has been drunk</p>b<p>Median split at 16 g alcohol</p

Demographic and clinical characteristics in male and female adolescents

1<p>“enriched” family adversity index as proposed by Rutter and Quinton measuring the presence of 11 adverse family factors covering characteristics of the parents, the partnership, and the family environment during a period of one year prior to birth</p>2<p>obstetric adversity score counting the presence of 9 adverse conditions during pregnancy, delivery, and postnatal period such as preterm labor, asphyxia or seizures</p

Comparisons of FDRs (BH) and p-values (P) for the BOMA-UTR and the GAIN-MGS data sets for the replicated pathways.

<p>* - Significant pathways identified by more than one pathway analysis method within the BOMA-UTR data set. The test statistics obtained using the alternative algorithms are provided in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004345#pgen.1004345.s004" target="_blank">Table S1B</a>.</p><p>Note: FDR – False Discovery Rate; BH – Benjamini-Hochberg.</p

Flowchart for (1) detection and replication of schizophrenia associated pathways and (2) identification of the most informative genes, and (3) functional annotation of single nucleotide polymorphisms in the genes of interest.

<p>Flowchart for (1) detection and replication of schizophrenia associated pathways and (2) identification of the most informative genes, and (3) functional annotation of single nucleotide polymorphisms in the genes of interest.</p

Description of individual samples.

a<p>Platforms are: I5, Illumina HumanHap 550; I6Q, Illumina Human610 Quad; IWQ, Illumina Human660W-Quad; A6, Affymetrix Genome-Wide Human SNP Array 6.0.</p>b<p>Publication reporting individual sample level genotypes for Schizophrenia is listed.</p><p>Discovery set: single nucleotide polymorphisms (SNPs) before pruning – 491,393; after pruning – 419,267.</p><p>Replication set: SNPs before pruning – 669,059; after pruning – 552,988.</p

RegulomeDB functional annotation for SNPs in CTCF and its regulatory regions.

<p>Notes: * genotyped in the BOMA-UTR data set and sorted by their genomic coordinates. SNPs are within or 20 kb upstream and downstream of <i>CTCF</i>. ** <i>AR FOXA1 USF1 CDX2 HNF4A TRIM28 USF2 TCF4 HDAC2 SP1 BHLHE40</i>. *** <i>KROX SP4 SP1:SP3 HIC1 Zif268 Sp4 Sp1 SP1 Egr</i>. § RegulomeDB score: [1f] - likely to affect binding and linked to expression of a gene target; [2b] - likely to affect binding; <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004345#pgen.1004345-Herold1" target="_blank">[4]</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004345#pgen.1004345-Wang1" target="_blank">[5]</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004345#pgen.1004345-Ramanan1" target="_blank">[6]</a> - minimum binding evidence.</p

Slope estimates (the change in log odds for a 1% increase in <i>Froh</i>; points) and their 95% confidence intervals (bars) of <i>Froh</i> from the combined unimputed SNP data predicting schizophrenia for different Mb thresholds of calling ROHs.

<p>All length thresholds longer than 1 Mb were significant.</p