Table 2.

List of SNPs in and around HLA region which surpassed genome-wide significance (p < 10⁻⁵) in our previous RA GWAS [13] and their significance status in the three Ayurveda sub-groups and total cohort.

SNP	Chr	Position	Gene	Location	Minor allele	PGWASTotal	OR (95% CI) Total	PGWASVata	OR (95% CI) Vata	PGWAS Pitta	OR (95% CI) Pitta	PGWAS Kapha	OR (95% CI) Kapha
rs9275406	6	32669955	HLA-DQB1	flanking_5UTR	T	0.004	1.66 (1.18–2.34)	0.09	2.75 (0.87–8.66)	0.008	1.88 (1.19–2.97)	0.55	1.23 (0.68–2.23)
rs9275388	6	32669084	HLA-DQB1	flanking_5UTR	C	0.004	1.65 (1.18–2.32)	0.09	2.75 (0.87–8.66)	0.01	1.84 (1.17–2.90)	0.46	1.26 (0.70–2.27)
rs9275390	6	32669156	HLA-DQB1	flanking_5UTR	C	0.004	1.65 (1.18–2.32)	0.09	2.75 (0.87–8.66)	0.01	1.84 (1.17–2.90)	0.46	1.26 (0.70–2.27)
rs9275407	6	32670037	HLA-DQB1	flanking_5UTR	T	0.003	1.67 (1.19–2.35)	0.09	2.75 (0.87–8.66)	0.008	1.88 (1.19–2.97)	0.46	1.26 (0.70–2.27)
rs9275393	6	32669439	HLA-DQB1	flanking_5UTR	A	0.005	1.63 (1.16–2.29)	0.14	2.63 (0.83–8.34)	0.01	1.82 (1.16–2.88)	0.46	1.26 (0.70–2.27)
rs9275425	6	32670874	HLA-DQB1	flanking_5UTR	A	0.005	1.63 (1.16–2.29)	0.09	2.75 (0.87–8.66)	0.01	1.77 (1.12–2.81)	0.46	1.28 (0.71–2.32)
rs9275439	6	32671521	HLA-DQB1	flanking_5UTR	C	0.003	1.67 (1.19–2.35)	0.09	2.75 (0.87–8.66)	0.01	1.84 (1.17–2.90)	0.46	1.31 (0.72–2.36)
rs9275427	6	32670915	HLA-DQB1	flanking_5UTR	T	–	–	–	–	–	–	–	–
rs9275374	6	32668526	HLA-DQB1	flanking_5UTR	T	0.004	1.65 (1.18–2.32)	0.09	2.75 (0.87–8.66)	0.01	1.84 (1.17–2.90)	0.46	1.26 (0.70–2.27)
rs9275418	6	32670244	HLA-DQB1	flanking_5UTR	G	0.005	1.64 (1.17–2.30)	0.14	2.63 (0.83–8.34)	0.01	1.84 (1.17–2.90)	0.46	1.26 (0.70–2.27)
rs9275428	6	32670978	HLA-DQB1	flanking_5UTR	G	0.007	1.62 (1.15–2.27)	0.09	2.75 (0.87–8.66)	0.01	1.79 (1.13–2.83)	0.55	1.23 (0.68–2.23)
rs9275424	6	32670576	HLA-DQB1	flanking_5UTR	G	0.008	1.57 (1.13–2.19)	0.06	2.94 (0.94–9.22)	0.04	1.62 (1.04–2.54)	0.46	1.30 (0.72–2.34)
rs9275371	6	32668296	HLA-DQB1	flanking_5UTR	C	–	–	–	–	–	–	–	–
rs9275595	6	32681355	HLA-DQA2	flanking_5UTR	C	0.007	1.63 (1.14–2.34)	0.20	2.38 (0.75–7.57)	0.01	1.94 (1.19–3.16)	0.75	1.14 (0.62–2.12)
rs9275582	6	32680070	HLA-DQA2	flanking_5UTR	T	0.007	1.63 (1.14–2.34)	0.20	2.38 (0.75–7.57)	0.01	1.94 (1.19–3.16)	0.75	1.14 (0.62–2.12)
rs2856725	6	32666738	HLA-DQB1	flanking_5UTR	C	0.09	0.78 (0.59–1.04)	0.14	0.57 (0.28–1.18)	0.77	0.93 (0.63–1.37)	0.10	0.62 (0.36–1.07)
rs2647012	6	32664458	HLA-DQB1	flanking_5UTR	T	0.08	0.77 (0.58–1.02)	0.13	0.55 (0.27–1.14)	0.70	0.91 (0.62–1.34)	0.11	0.63 (0.37–1.07)
rs2858305	6	32670464	HLA-DQB1	flanking_5UTR	G	0.08	0.78 (0.58–1.03)	0.13	0.55 (0.27–1.14)	0.69	0.92 (0.62–1.35)	0.11	0.64 (0.38–1.08)
rs2856717	6	32670308	HLA-DQB1	flanking_5UTR	A	0.10	0.78 (0.59–1.04)	0.13	0.55 (0.27–1.14)	0.77	0.94 (0.64–1.36)	0.11	0.63 (0.37–1.07)
rs10484561	6	32665420	HLA-DQB1	flanking_5UTR	G	0.004	1.99 (1.24–3.2)	0.06	6.54 (0.82–52.32)	0.00	2.5 (1.31–4.78)	1.00	1.06 (0.48–2.37)
rs7774434	6	32657578	HLA-DQB1	flanking_5UTR	T	0.02	0.72 (0.55–0.94)	0.05	0.47 (0.23–0.97)	0.23	0.79 (0.55–1.14)	0.11	0.65 (0.40–1.07)
rs13192471	6	32671103	HLA-DQB1	flanking_5UTR	C	0.01	1.74 (1.12–2.70)	0.03	7.94 (1.01–62.64)	0.03	1.89 (1.06–3.34)	1.00	1.06 (0.48–2.37)
rs9275572	6	32678999	HLA-DQA2	flanking_5UTR	A	0.09	0.78 (0.59–1.03)	0.20	0.6 (0.30–1.26)	0.63	0.90 (0.62–1.32)	0.11	0.63 (0.37–1.07)
rs9275596	6	32681631	HLA-DQA2	flanking_5UTR	C	0.01	0.65 (0.47–0.9)	0.01	0.36 (0.16–0.80)	1.00	0.97 (0.63–1.52)	0.00	0.38 (0.20–0.71)
rs13209234	6	32415975	HLA-DRA	flanking_3UTR	A	0.06	1.43 (0.99–2.06)	0.14	2.56 (0.81–8.10)	0.16	1.45 (0.88–2.39)	0.75	1.12 (0.59–2.12)
rs7755224	6	32652317	HLA-DQB1	flanking_5UTR	G	0.006	1.93 (1.21–3.08)	0.06	6.54 (0.82–52.32)	0.01	2.35 (1.25–4.44)	1.00	1.06 (0.48–2.37)
rs9391858	6	32341398	C6orf10	flanking_5UTR	G	0.06	1.42 (0.99–2.03)	0.09	2.75 (0.87–8.66)	0.26	1.35 (0.83–2.20)	rs9391858	1.20 (0.64–2.27)