Detailed phenotyping identifies genes with pleiotropic effects on body composition

BMC Genomics

Table 4 Total number of significant SNPs (P < 5 × 10⁻⁷), their FDR (%), and number of significant SNP on each chromosome (which is in parenthesis) for the 23 linear indexes corresponding to the 23 lead SNPs

Group^a	SNP order	Linear index^b code	Mapped^c gene code	Total No. SNP^d	FDR (%)	chromosome number (number of significant SNPs^e)
1	1st	OAR16_31.9 Mb	GHR	86	0.30	3 (1), 6 (83), 8 (1), 24 (1)
1	2nd	OAR14_34.8 Mb	LCAT
1	3rd	OAR11_26.4 Mb	SLC16A11	231	0.11	1 (2), 3 (1), 5 (2), 6 (218), 9 (4), 11 (2), 13 (2)
1	4 th	OAR6_37.5 Mb	LCORL	489	0.05	1 (3), 2 (1), 6 (475), 7 (1), 9 (2), 11 (6), 15 (1)
2	5th	OAR26_13.99 Mb	ACSL
2	6th	OAR11_13.3 Mb	ACACA	8	3.19	11 (6), 17 (2)
2	7th	OAR11_49.9 Mb	FASN	12	2.13	5 (1), 11 (6), 13 (4), 24 (1)
2	8th	OAR6_15.2 Mb	SNORA70	14	1.82	6 (12), 11 (1), 13 (1)
3	9th	OAR19_57.1 Mb	MRPS25	3	8.50	1 (1), 3 (2)
3	10th	OAR2_219.6 Mb	PLCD4	57	0.45	1 (3), 2 (54)
3	11th	OAR3_17.9 Mb	APOL6	3	8.50	3 (2), 23 (1)
3	12th	OAR5_93.4 Mb	CAST	5	5.10	3 (1), 5 (1), 11 (1), 21 (2)
3	13th	OAR18_64.5 Mb	MEG8_2	32	0.80	18 (32)
4	14 th	OAR8_25.0 Mb
4	15th	OAR22_20.3 Mb	PKD2L1	11	2.32	1 (1), 6 (2), 18 (8)
4	16th	OAR12_49.6 Mb	SAMD11	15	1.70	12 (14), 17 (1)
5	17th	OAR14_54.6 Mb	GYS1	10	2.55	2 (6), 4 (1), 10 (1), 18 (2)
5	18th	OAR3_21.9 Mb	PNPLA3
5	19th	OAR21_39.7 Mb	FADS2
5	20th	OAR19_30.8 Mb	5S-rRNA
5	21st	OAR20_44.1 Mb	SMIM13	9	2.83	20 (9)
5	22nd	OAR21_14.96 Mb
5	23rd	OAR15_47.5 Mb	U1	1	25.51	25 (1)

^a = Group of the lead SNPs that were clustered together as shown on Fig. 5
^b = 23 linear indexes corresponding to the 23 lead SNPs
^c = Genes located within 30 kb from each of lead SNPs excluding LCORL, and gene names are in Table 6
^d = Total number of significant SNPs which are significantly (P < 5 × 10⁻⁷) associated with each of linear indexes
^e = Number of significant SNP on each chromosome is in parentheses

ISSN: 1471-2164