Identification of five novel genetic loci related to facial morphology by genome-wide association studies

Cha, Seongwon; Lim, Ji Eun; Park, Ah Yeon; Do, Jun-Hyeong; Lee, Si Woo; Shin, Chol; Cho, Nam Han; Kang, Ji-One; Nam, Jeong Min; Kim, Jong-Sik; Woo, Kwang-Man; Lee, Seung-Hwan; Kim, Jong Yeol; Oh, Bermseok

doi:10.1186/s12864-018-4865-9

BMC Genomics

Table 4 Replication analysis of previous facial morphology GWASs

From: Identification of five novel genetic loci related to facial morphology by genome-wide association studies

Previously reported index SNP	Gene^a	Previously reported association phenotype	Reference	Tested SNP	LD (r²)^b	Coded allele	Non-coded allele	Associated facial traits in Phase 1	Association results
Previously reported index SNP	Gene^a	Previously reported association phenotype	Reference	Tested SNP	LD (r²)^b	Coded allele	Non-coded allele	Associated facial traits in Phase 1	beta ± se	P-value
rs7559271	PAX3	Nasion position,n-men	Adhikari, et al. [14] Paternoster et al. [12]	rs11683100	0.70	G	T	Profile nasal area	0.007 ± 0.004	0.043
rs4648379	PRDM16	AlrR-Prn, AlrL-Prn	Liu et al. [13]	rs4648478	0.65	G	A	Profile nasal angle	−0.005 ± 0.001	5.70 × 10^− 6
rs6555969	C5orf50	ZygR-Nsn,ZygL-Nsn,EyeR-Nsn,EyeL-Nsn	Liu et al. [13]	rs6555969	1.00	T	C	Right palpebrale fissure length	0.086 ± 0.069	0.210
rs805722	COL17A1	EyeR-Nsn,EyeL-Nsn	Liu et al. [13]	rs805693	0.97	T	C	Left palpebral fissure height	−0.039 ± 0.036	0.288
rs2045323	DCHS2	Columella inclination,Nose protrusion,Nose tip angle	Adhikari et al. [14]	rs4315762	0.68	G	C	Subnasal width	−0.247 ± 0.054	4.84 × 10⁻⁶
rs1852985	SUPT3H/RUNX2	Nose bridge breadth	Adhikari et al. [14]	rs1284964	1.00	G	A	Nasal bridge angle	0.429 ± 0.101	2.28 × 10⁻⁵
rs2424399	PAX1	Nasal width	Shaffer et al. [15]	rs6082475	1.00	G	A	Subnasal width	0.164 ± 0.049	7.28 × 10⁻⁴
rs9868698	SCHIP1	PC4(facial height, nasal width)	Cole et al. [16]	rs627865	0.98	G	C	Subnasal width	0.036 ± 0.051	0.485
rs2817419	TFAP2B	EX_R_EX_L(outer canthal width)	Cole et al. [16]	rs3857597	0.77	T	C	Outercanthal width	0.228 ± 0.138	0.098
rs35965172	TFAP2B	EN_EX(Palpebral fissure length)	Cole et al. [16]	rs3857597	0.78	T	C	Right eyelid width	0.011 ± 0.008	0.196
rs7836044	intergenic	STO_SL(lower lip height)	Cole et al. [16]	rs3850505	0.99	C	T	Left upper lip thickness	−0.006 ± 0.004	0.163
rs9456748	PARK2	factor 9(Facial height related to the vertical position of nasion; Nasion)	Lee et al. [17]	rs6904579	0.86	G	A	Facial height	−0.212 ± 0.099	0.033
rs5781117	LYPLAL1	nose size	Pickrell et al. [21]	rs2605100	0.78	T	C	Profile nasal angle	0.003 ± 0.001	0.030
rs424737	ROBO1	nose size	Pickrell et al. [21]	rs333472	1.00	C	T	Nasal tip height	0.007 ± 0.003	6.58 × 10⁻³
rs2929451	PPP1R3B	nose size	Pickrell et al. [21]	rs2929453	0.94	G	A	Nasal tip protrusion	−0.009 ± 0.007	0.212
rs10779169	RASSF9	nose size	Pickrell et al. [21]	rs2405254	0.99	T	A	Profile nasal angle	0.003 ± 0.001	8.30 × 10⁻³
rs11782517	MSRA	nose size	Pickrell et al. [21]	rs12544801	0.90	G	C	Nasolabial angle	−0.005 ± 0.003	0.081
rs767764	DLC1	nose size	Pickrell et al. [21]	rs2278945	0.71	G	A	Nasal bridge angle	−0.307 ± 0.092	8.94 × 10⁻⁴
rs34702092	RAD51B	nose size	Pickrell et al. [21]	rs11624333	1.00	G	A	Nasal bridge angle	−0.438 ± 0.156	5.02 × 10⁻³
rs6101567	DHX35	nose size	Pickrell et al. [21]	rs6129346	0.99	C	T	Frontal nasal height	−0.299 ± 0.076	7.53 × 10⁻⁵

AlrL alare left, AlrR alare right, Prn pronasale, ZygL zygion left, ZygR zygion right, Nsn nasion, EyeL eyeball left, EyeR eyeball right
^aGenes are defined as previously reported
^br² is calculated based on data from phase 3 of the 1000 Genomes Project in the Asian panel (Chinese and Japanese)

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