The effect of measurement error of phenotypes on genome wide association studies

BMC Genomics

Table 2 Summary of genome wide associations for CHILLP8 and P8FAT under different kinds of trimming.

Trait	Type	N SNP^A	FPR^B	Common Sig SNPs^C	r ^D	Top 5 Chr^E	Sig %^F	Best region^G	Gene(s)^H
CHILLP8	GWAS	63	84%	-	-	14, 7, 8, 1, 6	42.9%	BTA14:23	XKR4 to PENK including PLAG1
P8FAT	GWAS	71	76%	7	0.53	14, 9, 6, 8, 7	45.1%	BTA14:25	NSMAF & TOX
P8MEAN	GWAS	59	92%	22/23^I	0.84/0.88^I	14, 8, 6, 3, 13	55.9%	BTA14:23 & 25	XKR4 to TOX
CHILLP8	trim10%	57	95%	-	-	14, 1, 11, 3, 22	38.6%	BTA14:23	XKR4 to PENK
P8FAT	trim10%	66	82%	0	0.38	14, 9, 29, 11, 10	47.0%	BTA14:25	NSMAF & TOX
CHILLP8	diff < 36	53	100%	-	-	14, 8, 3, 18, 13	45.2%	BTA14:23 & 25	XKR4 to TOX
P8FAT	diff < 36	52	100%	10	0.75	14, 2, 3, 1, 8	42.3%	BTA14:23 & 25	XKR4 to TOX
CHILLP8	diff < 4	81	67%	-	-	14, 11, 1, 2, 7	48.1%	BTA14:23 & 25	XKR4 to TOX
P8FAT	diff < 4	98	55%	49	0.92	14, 11, 15, 2, 6	45.0%	BTA14:23 & 25	XKR4 to TOX

^A Number SNP significant at P < 0.001
^B False positive rate
^C Number of significant (P < 0.001) SNP in common between a CHILLP8 and P8FAT GWAS of the same type
^D Correlation between allele effects of GWAS of CHILLP8 and P8FAT for the same method of data trimming
^E Top 5 chromosomes with largest number of SNP significant at P < 0.001 in descending order of number of significant SNP
^F Percent of SNP with P < 0.001 on the top 5 chromosomes compared to all chromosomes
^G Genomic region with the largest number of SNP significant at P < 0.001
^H Gene(s) located to this genomic region
^I P8MEAN and CHILLP8 or P8FAT respectively

ISSN: 1471-2164