Polymorphism rs143384 GDF5 reduces the risk of knee osteoarthritis development in obese individuals and increases the disease risk in non-obese population

Table 3 Regulatory effects of the KOA-associated polymorphism rs143384 and SNPs in high LD (r² ≥ 0.80) (data of the Haploreg database)

Chr	Position (hg38)	LD		variant	Ref	Alt	EUR frequency	Conserved sequence (SiPhy algoritm)	Promoter histone marks	Enhancer histone marks	DNase hypersensitive site	Proteins bound	Motifs changed	NHGRI/EBI GWAS hits	GRASP QTL hits	Selected eQTL hits	GENCODE genes	dbSNP Base (functional annotation)
Chr	Position (hg38)	r²	D	variant	Ref	Alt	EUR frequency	Conserved sequence (SiPhy algoritm)	Promoter histone marks	Enhancer histone marks	DNase hypersensitive site	Proteins bound	Motifs changed	NHGRI/EBI GWAS hits	GRASP QTL hits	Selected eQTL hits	GENCODE genes	dbSNP Base (functional annotation)
20	35414469	0.8	-0.94	rs34091597	CAT	C	0.61						Foxa, TFE			24 hits	2.3 kb 5’ of UQCC
20	35417411	0.81	-0.95	rs6060401	C	T	0.62						Ets, Pitx2			55 hits	5.3 kb 5’ of UQCC
20	35417437	0.81	-0.95	rs6060402	T	C	0.62						SP2			64 hits	5.3 kb 5’ of UQCC
20	35419167	0.8	-0.94	rs6141551	T	C	0.61						LUN-1			54 hits	7 kb 5’ of UQCC
20	35420334	0.81	-0.95	rs7262358	C	T	0.62						4 altered motifs			57 hits	8.2 kb 5’ of UQCC
20	35420820	0.81	-0.95	rs6142381	G	A	0.62						9 altered motifs			55 hits	8.7 kb 5’ of UQCC
20	35431781	0.84	0.98	rs224329	C	T	0.38		LIV	5 tissues	4 tissues		EBF	1 hit	1 hit	63 hits	1.2 kb 5’ of GDF5OS
20	35436182	0.83	0.99	rs224333	G	A	0.37	+	7 tissues	6 tissues	ESDR		4 altered motifs	1 hit		57 hits	GDF5	intronic
20	35437976	1	1	rs143384	A	G	0.41	+	9 tissues	13 tissues	16 tissues		Ascl2	3 hits		47 hits	GDF5	5’-UTR
		0.85	0.99	rs78110303	A	G	0.37	+	9 tissues	14 tissues	31 tissues		4 altered motifs			24 hits	GDF5	5’-UTR

Chr Chromosome, LD linkage disequilibrium, r² Pearson correlation coefficient, D linkage disequilibrium coefficient, Ref reference allele, Alt alternative allele

ISSN: 2524-7948