Exploring quantitative traits-associated copy number deletions through reanalysis of UK10K consortium whole genome sequencing cohorts

Table 2 Copy number deletions with sub-threshold associations with traits replicated at the other cohort

Position*	Trait(unit)	Subject No.	Beta(S.E) _discovery **	P_discovery/ P_replication***	P_{meta−analysis}	Genetic model	Cohort_discovery	Cohort_discovery MAF (Homozygote count:Ref,Del)	gnomAD MAF (gnomAD ID) ****	RefSeq Gene	annotation
4:187093507–187,098,168 (nssv15897230)	FVC(L)	1,606	-0.06(0.02)	8.03E-04/ 4.92E-02	1.62E-04	additive	TwinsUK	0.56(332,546)	0.63	FAM149A	3’UTR(exon14-txEnd)
5:21611834–21,614,796 (nssv15898821)	Total Fat Mass (kg,9 year)	1,703	1.26(0.30)	1.79E-04 (2.52E-05^#)/ 3.79E-02	3.88E-05^##	additive	ALSPAC	0.08(1574,12)	0.08	GUSBP1	Enhancer
5:21611834–21,614,796 (nssv15898821)	Waist Circumference (kg)	1,812	1.72(0.44)	8.18E-04/ 4.35E-03	1.10E-05^##	additive	ALSPAC	0.08(1574,12)	0.08	GUSBP1	Enhancer
3:141572125–141,572,896 (nssv15883024)	Hemoglobin (g/L,9 year)	1,524	-2.28(0.61)	1.82E-04/ 1.10E-02	9.11E-06^##	additive	ALSPAC	0.09(1559/17)	0.08	ATP1B3;GK5 ;GRK7;RASA2;RNF7;TRPC1;XRN1;ZBTB38	Enhancer
4:172988628–172,992,939 (nssv15893853)	Heart rate (/min,13 year)	1,597	-1.63(0.42)	9.10E-05/ 4.43E-02	9.02E-05	additive	ALSPAC	0.49(476,454)	0.51	GALNTL6	Intron 2
1:243782752–243,783,761 (nssv15850019)	HOMA beta	1,580	17.16(9.07)	7.47E-04/ 4.96E-02	1.29E-04	dominant	TwinsUK	0.69(163,844)	0.66	AKT3	Intron 5
2:123364888–123,365,356 (nssv15869944)	TRIG (mmol/L,9 year)	1,497	-0.10(0.03)	2.69E-04/ 4.55E-02	7.83E-05	recessive	ALSPAC	0.63(242,712)	0.62		Intergenic

*Reference sequence is GRCh37.
**calculated by GWAS of traits before variable transformation
***P values are adjusted for age and sex after rank-based normal transformation of traits
****gnomAD SV allele frequency in Europeans
# untransformed, ## Bonferroni-corrected genome-wide significant

ISSN: 1471-2164