6 CHAPTER 6 126 Figure 3 Gene-based Manhattan plot Input SNPs were mapped to 18,795 protein coding genes. The horizontal axis shows the chromosomal position and the vertical axis shows the significance of tested markers. The threshold for genome wide significance (p = 0.05/18,795 = 2.66 x 10-6) is indicated by a dotted line. Table 2 SNPs at the four loci associated with cluster headache discovery sample SNP Chr:Pos EA:NEAa EAF OR [95% CI] P-valueb Nearest Genec eQTL mapped genesd rs11579212 1:222072819 C:A 0.34 1.51 [1.33-1.72] 4.78 x 10-10 RP11-815M8.1 DUSP10 rs6541998 2:112785237 C:T 0.63 1.53 [1.37-1.74] 1.91 x 10-10 MERTK TTL POLR1B FBLN7 ZC3H8 MERTK TMEM87 RGPD8 ZC3H6 rs10184573 2:200448253 T:G 0.44 1.43 [1.26-1.61] 2.20 x 10-8 AC093590.1 SATB2 FTCDNL1 rs2499799 6:96851676 C:T 0.81 0.62 [0.54-0.73] 1.29 x 10-9 UFL1/FHL5 UFL1 FHL5 GPR63 MMS22L FUT9 a Chromosomal positions in GRCh37/hg19 coordinates. b Significant result (p < 5 x 10-8). c The nearest gene is based on ANNOVAR annotations with Ensembl build 85. d eQTL mapping was done in FUMA based on GTEx v8. SNP = single nucleotide polymorphism; Chr = chromosome; Pos = position; EA = effect allele; NEA = non effect allele; EAF = effect allele frequency; OR = odds ratio; CI = confidence interval
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