Previously, eight spacer sequences in the CRISPR loci of S. solfataricus P2 were identified that matched perfectly to SMV1, one located in locus A (spacer 38) and seven in locus D (spacers 24, 26, 34, 35, 37, 39 and 40) and each exhibiting cognate PAM sequences [ 24, 24a].
We searched for GWAS-traits enriched for eSNPs located in loci of pseudogene and loci of ncRNAs.
We found 17 GWAS-traits nominally enriched for eSNPs located in loci of ncRNAs (Supplementary Material, Table S8) and 14 GWAS-traits nominally enriched for eSNPs located in loci of pseudogenes (Supplementary Material, Table S9).
In contrast, world-wide distributed risk alleles appear to be located in loci that do not show population-specific patterns of genetic variability.
Among these candidates, two SNPs, STAT4 rs10931468 and IRF5 rs12531711, located in loci reproducibly strongly associated with SSc in several studies [ 3, 4], were excluded from the study.
None of 33 miRNAs are located in loci for the other top candidate genes such as 8p12 (WRN), 9q22 (SYK), or 4p16 (ADRA2C).
It is also notable that many disease-associated variants identified by GWAS are located in loci that have previously been linked to Mendelian diseases (Lupski et al., 2011).
Our analysis indicates that markers located in loci known to influence fat mass through increased appetite affect obesity in Saudi Arabians to an extent possibly greater than in Europeans.
Cell bodies of noradrenergic neurons projecting to the VTA are located in the locus coeruleus [63], and electrical stimulation of the locus coeruleus has been shown to excite dopaminergic cell bodies in the VTA [64].
An important tumor suppressor gene located in this locus is RUNX3 which is often deleted or hypermethylated in various cancers showing epithelial, hematopoietic, and neural phenotypes [24].
The associated IL23R SNPs are shown in Table 2. Of the remaining 49 index SNPs, associations were replicated with 25 SNPs (p<0.05) with 15 of them previously identified as CD specific (including rs2188962 located in IBD5 locus) (Table 1).
