Table 1 Sequence variants at the LAG3 locus that associated with LAG-3 protein levels in plasma (top cis-pQTL) and their association with risk of autoimmune thyroid disease

From: Start codon variant in LAG3 is associated with decreased LAG-3 expression and increased risk of autoimmune thyroid disease

Chrom

Pos

rs

Variant effect

EA

OA

SomaScan (Iceland)*

AITD meta-analysis**

37,943 individuals

110,945 cases; 1,084,290 controls

MAF (%)

effect in SD (adj.)***

P

MAF (%)

OR

P

chr12

6772551

rs781745126

5′-UTR

T

C

0.13

−1.62

3 × 10−44

0.07

3.42

2 × 10−16

chr12

6773332

rs149722682

Pro67Thr

A

C

0

–

–

0.10

2.11

2 × 10−9

chr12

6774733

rs147749635

Pro217Leu

T

C

0.13

−1.31

1 × 10−30

0.06

1.27

0.03

chr12

6771308

rs7488113

upstream

T

G

2.48

−0.17

1 × 10−9

3.80

0.98

0.07

chr12

6775910

rs3782735

downstream

G

A

38.27

−0.13

1 × 10−51

40.95

0.99

0.28

chr12

6771830

rs2301333

upstream

A

G

5.94

0.13

1 × 10−13

5.72

0.98

0.12

  1. *The Somascan dataset is an Icelandic cohort of cases and controls (irrespective of diseases) that had available plasma samples (N = 39,155) and of those, 37,943 also had genotypes and overlaps with the Icelandic cohort of AITD cases and controls (see further description in ref. Ferkingstad, E. et al. Large-scale integration of the plasma proteome with genetics and disease, Nat Genet 2021).
  2. **GWAS meta-analysis of study populations from Iceland (18,651 cases and 326,068 controls), UK (33,822 cases and 396,901 controls), Finland (Finngen release 8: 36,321 cases and 306,178 controls) and USA (22,151 cases and 55,143 controls), in total 110,945 cases and 1,084,290 controls. We used logistic regression analysis assuming a multiplicative model, reporting odds ratios (OR) and two-sided P-values adjusted for year of birth, sex and origin (Iceland) or the first principal components (UK, USA) and Bonferroni adjustments for multiple comparisons, see further in Supplementary Data 1 and 9 and Methods. rs781745126 is only present in Iceland and rs149722682 in Finland.
  3. ***Effect is adjusted for the lead signal at the locus.
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