Associations of single nucleotide polymorphisms with mucinous colorectal cancer: genome-wide common variant and gene-based rare variant analyses

Table 4 Most significant gene regions identified from SKAT-O multivariable analysis

Genomic location^a	Gene^b	Description^c	Other genes in the gene-based region^d	# of SNPs	SNPs	P-value
Chr4:110349928–110467052	SEC24B	protein coding	SEC24B-AS1 (partial sequence)	5	rs10516557, kgp21293502, rs10003981, rs17040515, rs17040519	1.81E-05
Chr4:110476361–110614874	CCDC109B	protein coding	CDC42P4 (pseudogene: partial sequence), HIGD1AP14 (pseudogene; full length), CASP6 (partial sequence)	6	rs17619262, rs7654187, rs6831048, rs17619310, rs9997940, rs1053680	3.29E-05
Chr14:24386456–24408777	LINC00596	long intergenic non-protein coding RNA	DHRS4-AS1 (partial sequence)	6	rs8010486, rs1159372, rs10135026, rs8005541, rs8019962, kgp19564619	3.34E-05
Chr4:110263631–110359973	SEC24B-AS1	noncoding RNA; antisense RNA	RBMXP4 (pseudogene; full length), SEC24B (partial sequence)	7	rs10031399, rs17040364, rs17040369, rs11098033, rs17040401, rs12648138, rs11098035	4.21E-05
Chr1:207074273–207084738	RP11-564A8.8	pseudogene	IL24 (partial sequence), FAIM3 (partial sequence), FCMR (partial sequence)	10	rs3093428, kgp15249933, kgp15191074, rs3093447, kgp22852559, rs3093434, rs3093437, rs3093438, rs3093440, rs41304091	5.47E-05
Chr8:320931–338174	FAM87A	non-coding RNA	–	7	rs4527844, kgp20525414, kgp20198205, rs11785854, rs7461388, rs17064450, rs17064458	6.58E-05

^aThese genomic locations describe the region containing the gene as well as 5 kb long sequences before and after the gene. ^bBased on the information in the UCSC database [62]. ^cNCBI’s Gene Entrez database [77]. ^dIn some cases, the gene regions examined also contained sequences of other genes. Chr chromosome

ISSN: 2050-7771