fcfdr: an R package to leverage continuous and binary functional genomic data in GWAS

BMC Bioinformatics

Table 1 Table of newly significant index SNPs from type 1 diabetes application

rsID	Position	Ref/Alt	OR	SE	p value	v-value	RA p value	DGF	H3K27ac percentile	Gene
rs1052553	chr17:44073889	A/G	0.889	0.022	\(8.16\times 10^{-8}\)	\(3.10\times 10^{-8}\)	\(6.76\times 10^{-3}\)	1	2.2th	STH
rs3024505	chr1:206939904	G/A	0.864	0.027	\(6.39\times 10^{-8}\)	\(4.51\times 10^{-8}\)	0.601	1	87.4th	IL19
rs6518350	chr21:45621817	A/G	0.880	0.024	\(9.64\times 10^{-8}\)	\(4.26\times 10^{-8}\)	0.062	0	72.7th	ICOSLG
rs13415583	chr2:100764087	T/G	0.904	0.019	\(1.06\times 10^{-7}\)	\(4.81\times 10^{-8}\)	\(1.91\times 10^{-6}\)	0	14.4th	AFF3

For each of the four newly significant SNPs from the cFDR analysis, we list the rsID, genomic position (hg19; Position), reference and alternative alleles (Ref/Alt), odds ratio (OR), standard error (SE) and p value reported in the primary GWAS data set [18], v-value from the cFDR analysis, GWAS p value for rheumatoid arthritis [27] (RA p value), binary indicator of SNP overlap with regulatory factor binding sites (DGF), percentile of mean H3K27ac fold change value across asthma relevant cell types (H3K27ac percentile) and the closest protein-coding gene

ISSN: 1471-2105